fhR-4.4.2-foss-2024a-R-4.4.2.eb

Known Issues

None

Package List

ALDEx2-1.38.0 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
ALL 1.46.0 Package Not Found
AgiMicroRna-2.56.0 Processing and Differential Expression Analysis of Agilent microRNA chips
AnnotationDbi-1.68.0 Manipulation of SQLite-based annotations in Bioconductor
AnnotationFilter-1.30.0 Facilities for Filtering Bioconductor Annotation Resources
AnnotationForge-1.48.0 Tools for building SQLite-based annotation data packages
AnnotationHub-3.14.0 Client to access AnnotationHub resources
ArchR 1.0.2 Package Not Found
BSgenome-1.74.0 Software infrastructure for efficient representation of full genomes and their SNPs
BSgenome.Hsapiens.UCSC.hg19 1.4.3 Package Not Found
Bhat-0.9-12 General Likelihood Exploration
Biobase-2.66.0 Biobase: Base functions for Bioconductor
BiocBaseUtils-1.8.0 General utility functions for developing Bioconductor packages
BiocFileCache-2.14.0 Manage Files Across Sessions
BiocGenerics-0.52.0 S4 generic functions used in Bioconductor
BiocIO-1.16.0 Standard Input and Output for Bioconductor Packages
BiocManager-1.30.25 Access the Bioconductor Project Package Repository
BiocNeighbors-2.0.1 Nearest Neighbor Detection for Bioconductor Packages
BiocParallel-1.40.0 Bioconductor facilities for parallel evaluation
BiocSingular-1.22.0 Singular Value Decomposition for Bioconductor Packages
BiocStyle-2.34.0 Standard styles for vignettes and other Bioconductor documents
BiocVersion-3.20.0 Set the appropriate version of Bioconductor packages
Biostrings-2.74.1 Efficient manipulation of biological strings
BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
Bolstad-0.2.42 Functions for Elementary Bayesian Inference
Bolstad2-1.0-29 Bolstad Functions
BradleyTerry2-1.1-2 Bradley-Terry Models
CATALYST-1.30.2 Cytometry dATa anALYSis Tools
CGHbase-1.66.0 CGHbase: Base functions and classes for arrayCGH data analysis.
CLONETv2-2.2.1 Clonality Estimates in Tumor
CMA-1.64.0 Synthesis of microarray-based classification
CNEr-1.42.0 CNE Detection and Visualization
COMPASS-1.44.0 Combinatorial Polyfunctionality Analysis of Single Cells
CaSpER v2.0 Package Not Found
Category-2.72.0 Category Analysis
ChIPQC-1.42.0 Quality metrics for ChIPseq data
ChIPpeakAnno-3.40.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
ChIPseeker-1.42.1 ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ComplexHeatmap-2.22.0 Make Complex Heatmaps
ConsensusClusterPlus-1.70.0 ConsensusClusterPlus
CytoML-2.18.2 A GatingML Interface for Cross Platform Cytometry Data Sharing
DAAG-1.25.6 Data Analysis and Graphics Data and Functions
DECIPHER-3.2.0 Tools for curating, analyzing, and manipulating biological sequences
DEGseq-1.60.0 Identify Differentially Expressed Genes from RNA-seq data
DESeq2-1.46.0 Differential gene expression analysis based on the negative binomial distribution
DNAcopy-1.80.0 DNA Copy Number Data Analysis
DO.db 2.9 Package Not Found
DOSE-4.0.0 Disease Ontology Semantic and Enrichment analysis
DOT-0.1 Render and Export DOT Graphs in R
DelayedArray-0.32.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
DelayedMatrixStats-1.28.1 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
DiceDesign-1.10 Designs of Computer Experiments
DiffBind-3.16.0 Differential Binding Analysis of ChIP-Seq Peak Data
DirichletMultinomial-1.48.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
DynDoc-1.84.0 Dynamic document tools
EBImage-4.48.0 Image processing and analysis toolbox for R
EpiModel-2.5.0 Mathematical Modeling of Infectious Disease Dynamics
ExperimentHub-2.14.0 Client to access ExperimentHub resources
FDb.InfiniumMethylation.hg19 2.2.0 Package Not Found
FlowSOM-2.14.0 Using self-organizing maps for visualization and interpretation of cytometry data
GEOquery-2.74.0 Get data from NCBI Gene Expression Omnibus (GEO)
GO.db 3.19.1 Package Not Found
GOSemSim-2.32.0 GO-terms Semantic Similarity Measures
GOstats-2.72.0 Tools for manipulating GO and microarrays
GPfit-1.0-8 Gaussian Processes Modeling
GSEABase-1.68.0 Gene set enrichment data structures and methods
GSVA-2.0.5 Gene Set Variation Analysis for Microarray and RNA-Seq Data
GWASExactHW-1.2 Exact Hardy-Weinburg Testing for Genome Wide Association Studies
GWASTools-1.52.0 Tools for Genome Wide Association Studies
GenomeInfoDb-1.42.3 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
GenomeInfoDbData 1.2.12 Package Not Found
GenomicAlignments-1.42.0 Representation and manipulation of short genomic alignments
GenomicFeatures-1.58.0 Query the gene models of a given organism/assembly
GenomicFiles-1.42.0 Distributed computing by file or by range
GenomicRanges-1.58.0 Representation and manipulation of genomic intervals
Glimma-2.16.0 Interactive visualizations for gene expression analysis
Gmisc-3.0.3 Descriptive Statistics, Transition Plots, and More
GreyListChIP-1.38.0 Grey Lists – Mask Artefact Regions Based on ChIP Inputs
Gviz-1.50.0 Plotting data and annotation information along genomic coordinates
HDF5Array-1.34.0 HDF5 datasets as array-like objects in R
HDO.db 0.99.1 Package Not Found
HMMcopy-1.48.0 Copy number prediction with correction for GC and mappability bias for HTS data
HSMMSingleCell 1.24.0 Package Not Found
HaploSim-1.8.4.2 Functions to Simulate Haplotypes
Homo.sapiens 1.3.1 Package Not Found
IHW-1.34.0 Independent Hypothesis Weighting
IRanges-2.40.1 Foundation of integer range manipulation in Bioconductor
IRdisplay-1.1 ‘Jupyter’ Display Machinery
IlluminaHumanMethylation450kmanifest 0.4.0 Package Not Found
InteractionSet-1.34.0 Base Classes for Storing Genomic Interaction Data
KEGGREST-1.46.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
KEGGgraph-1.66.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
LogicReg-1.6.6 Logic Regression
LymphoSeq-1.34.0 Analyze high-throughput sequencing of T and B cell receptors
LymphoSeqDB 0.99.2 Package Not Found
MAGeCKFlute-2.9.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
MAST-1.32.0 Model-based Analysis of Single Cell Transcriptomics
MCMCglmm-2.36 MCMC Generalised Linear Mixed Models
MPV-1.64 Data Sets from Montgomery, Peck and Vining
MatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
MatrixExtra-0.1.15 Extra Methods for Sparse Matrices
MatrixGenerics-1.18.1 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
Mfuzz-2.66.0 Soft clustering of omics time series data
NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
NOISeq-2.50.0 Exploratory analysis and differential expression for RNA-seq data
Nozzle.R1-1.1-1.1 Nozzle Reports
OrganismDbi-1.48.0 Software to enable the smooth interfacing of different database packages
PBSddesolve-1.13.4 Solver for Delay Differential Equations
PFAM.db 3.19.1 Package Not Found
PICS-2.50.0 Probabilistic inference of ChIP-seq
PolynomF-2.0-8 Polynomials in R
ProtGenerics-1.38.0 Generic infrastructure for Bioconductor mass spectrometry packages
QUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix Estimation
R2jags-0.8-9 Using R to Run ‘JAGS’
RBGL-1.82.0 An interface to the BOOST graph library
REDCapR-1.4.0 Interaction Between R and REDCap
RLRsim-3.1-8 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models
RNASeqPower-1.46.0 Sample size for RNAseq studies
RPostgres-1.4.8 C++ Interface to PostgreSQL
RPresto-1.4.7 DBI Connector to Presto
RProtoBuf-0.4.23 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)
RProtoBufLib-2.18.0 C++ headers and static libraries of Protocol buffers
RSclient-0.7-10 Client for Rserve
RVenn-1.1.0 Set Operations for Many Sets
RaggedExperiment-1.30.0 Representation of Sparse Experiments and Assays Across Samples
RcppAnnoy-0.0.22 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest Neighbors
RcppCCTZ-0.2.13 ‘Rcpp’ Bindings for the ‘CCTZ’ Library
RcppDate-0.0.5 ‘date’ C++ Header Library for Date and Time Functionality
RcppHNSW-0.6.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest Neighbors
RcppML-0.3.7 Rcpp Machine Learning Library
RcppNumerical-0.6-0 ‘Rcpp’ Integration for Numerical Computing Libraries
RcppPlanc 1.0.0 Package Not Found
RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG Implementations
Rdsdp-1.0.5.2.1 R Interface to DSDP Semidefinite Programming Library
ReportingTools-2.46.0 Tools for making reports in various formats
Rfast-2.1.5 A Collection of Efficient and Extremely Fast R Functions
Rgraphviz-2.50.0 Provides plotting capabilities for R graph objects
Rhdf5lib-1.28.0 hdf5 library as an R package
Rhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’
Rhtslib-3.2.0 HTSlib high-throughput sequencing library as an R package
Rlabkey-3.4.1 Data Exchange Between R and ‘LabKey’ Server
Rmpi-0.7-3.3 Interface (Wrapper) to MPI (Message-Passing Interface)
Rsamtools-2.22.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Rsubread-2.20.0 Mapping, quantification and variant analysis of sequencing data
S4Arrays-1.6.0 Foundation of array-like containers in Bioconductor
S4Vectors-0.44.0 Foundation of vector-like and list-like containers in Bioconductor
SNPRelate-1.40.0 Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
SNPassoc-2.1-2 SNPs-Based Whole Genome Association Studies
SPIA-2.58.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
ScaledMatrix-1.14.0 Creating a DelayedMatrix of Scaled and Centered Values
SemiPar-1.0-4.2 Semiparametic Regression
ShortRead-1.64.0 FASTQ input and manipulation
SingleCellExperiment-1.28.1 S4 Classes for Single Cell Data
SparseArray-1.6.2 High-performance sparse data representation and manipulation in R
SpatialExperiment-1.16.0 S4 Class for Spatially Resolved -omics Data
SummarizedExperiment-1.36.0 A container (S4 class) for matrix-like assays
TFBSTools-1.44.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
TFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight Matrices
TitanCNA-1.44.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
TxDb.Celegans.UCSC.ce6.ensGene 3.2.2 Package Not Found
TxDb.Dmelanogaster.UCSC.dm3.ensGene 3.2.2 Package Not Found
TxDb.Hsapiens.UCSC.hg18.knownGene 3.2.2 Package Not Found
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 Package Not Found
TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0 Package Not Found
TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2 Package Not Found
TxDb.Rnorvegicus.UCSC.rn4.ensGene 3.2.2 Package Not Found
UCSC.utils-1.2.0 Low-level utilities to retrieve data from the UCSC Genome Browser
VariantAnnotation-1.52.0 Annotation of Genetic Variants
Wrench-1.24.0 Wrench normalization for sparse count data
XVector-0.46.0 Foundation of external vector representation and manipulation in Bioconductor
affxparser-1.78.0 Affymetrix File Parsing SDK
affy-1.84.0 Methods for Affymetrix Oligonucleotide Arrays
affycoretools-1.78.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
affyio-1.76.0 Tools for parsing Affymetrix data files
alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
amap-0.8-20 Another Multidimensional Analysis Package
annaffy-1.78.0 Annotation tools for Affymetrix biological metadata
annotate-1.84.0 Annotation for microarrays
apeglm-1.28.0 Approximate posterior estimation for GLM coefficients
argparser-0.7.2 Command-Line Argument Parser
arsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical Summaries
arules-1.7-9 Mining Association Rules and Frequent Itemsets
ash-1.0-15 David Scott’s ASH Routines
ashr-2.2-63 Methods for Adaptive Shrinkage, using Empirical Bayes
assorthead-1.0.1 Assorted Header-Only C++ Libraries
aws.ec2metadata-0.2.0 Get EC2 Instance Metadata
aws.s3-0.3.21 ‘AWS S3’ Client Package
aws.signature-0.6.0 Amazon Web Services Request Signatures
babelgene-22.9 Gene Orthologs for Model Organisms in a Tidy Data Format
bamsignals-1.38.0 Extract read count signals from bam files
base64url-1.4 Fast and URL-Safe Base64 Encoder and Decoder
basilisk-1.18.0 Freezing Python Dependencies Inside Bioconductor Packages
basilisk.utils-1.18.0 Basilisk Installation Utilities
batchtools-0.9.17 Tools for Computation on Batch Systems
beachmat-2.22.0 Compiling Bioconductor to Handle Each Matrix Type
benchmark-0.3-6 Benchmark Experiments Toolbox
bezier-1.1.2 Toolkit for Bezier Curves and Splines
biglm-0.9-3 Bounded Memory Linear and Generalized Linear Models
biomaRt-2.62.1 Interface to BioMart databases (i.e. Ensembl)
biomformat-1.34.0 An interface package for the BIOM file format
biovizBase-1.54.0 Basic graphic utilities for visualization of genomic data.
bookdown-0.42 Authoring Books and Technical Documents with R Markdown
breakaway-4.8.4 Species Richness Estimation and Modeling
bumphunter-1.48.0 Bump Hunter
catdata-1.2.4 Categorical Data
chipseq-1.56.0 chipseq: A package for analyzing chipseq data
chromVAR-1.28.0 Chromatin Variation Across Regions
clusterProfiler-4.14.6 A universal enrichment tool for interpreting omics data
collections-0.3.7 High Performance Container Data Types
colorRamps-2.3.4 Builds Color Tables
compare-0.2-6 Comparing Objects for Differences
config-0.3.2 Manage Environment Specific Configuration Values
cummeRbund-2.48.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
curry-0.1.1 Partial Function Application with %<%, %-<%, and %><%
cyclocomp-1.1.1 Cyclomatic Complexity of R Code
cytolib-2.16.0 C++ infrastructure for representing and interacting with the gated cytometry data
dada2-1.34.0 Accurate, high-resolution sample inference from amplicon sequencing data
degreenet-1.3-6 Models for Skewed Count Distributions Relevant to Networks
densvis-1.16.0 Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
depmap 1.18.0 Package Not Found
derfinder-1.40.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
derfinderHelper-1.40.0 derfinder helper package
descr-1.1.8 Descriptive Statistics
dfoptim-2023.1.0 Derivative-Free Optimization
dials-1.4.0 Tools for Creating Tuning Parameter Values
diamonds-1.0-5 Analysis and sampling grids from diamond partitions
diffusionMap-1.2.0 Diffusion Map
dir.expiry-1.14.0 Managing Expiration for Cache Directories
directlabels-2024.1.21 Direct Labels for Multicolor Plots
doFuture-1.0.1 Use Foreach to Parallelize via the Future Framework
doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
dqrng-0.4.1 Fast Pseudo Random Number Generators
drc-3.0-1 Analysis of Dose-Response Curves
edgeR-4.4.2 Empirical Analysis of Digital Gene Expression Data in R
egor-1.24.2 Import and Analyse Ego-Centered Network Data
elasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCA
enrichplot-1.26.6 Visualization of Functional Enrichment Result
ensembldb-2.30.0 Utilities to create and use Ensembl-based annotation databases
ergm.ego-1.1.0 Fit, Simulate and Diagnose Exponential-Family Random Graph Models to Egocentrically Sampled Network Data
etrunct-0.1 Computes Moments of Univariate Truncated t Distribution
europepmc-0.4.3 R Interface to the Europe PubMed Central RESTful Web Service
fANCOVA-0.6-1 Nonparametric Analysis of Covariance
faraway-1.0.9 Datasets and Functions for Books by Julian Faraway
fastseg-1.52.0 fastseg - a fast segmentation algorithm
fasttime-1.1-0 Fast Utility Function for Time Parsing and Conversion
fda-6.2.0 Functional Data Analysis
fds-1.8 Functional Data Sets
fgsea-1.32.2 Fast Gene Set Enrichment Analysis
filelock-1.0.3 Portable File Locking
fit.models-0.64 Compare Fitted Models
float-0.3-2 32-Bit Floats
flowClust-3.44.0 Clustering for Flow Cytometry
flowCore-2.18.0 flowCore: Basic structures for flow cytometry data
flowStats-4.18.0 Statistical methods for the analysis of flow cytometry data
flowViz-1.70.0 Visualization for flow cytometry
flowWorkspace-4.18.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
forestplot-3.1.6 Advanced Forest Plot Using ‘grid’ Graphics
forge-0.2.0 Casting Values into Shape
fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
gage-2.56.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
gcrma-2.78.0 Background Adjustment Using Sequence Information
gdsfmt-1.42.1 R Interface to CoreArray Genomic Data Structure (GDS) Files
geneLenDataBase 1.39.0 Package Not Found
genefilter-1.88.0 genefilter: methods for filtering genes from high-throughput experiments
geneplotter-1.84.0 Graphics related functions for Bioconductor
ggVennDiagram-1.5.2 A ‘ggplot2’ Implement of Venn Diagram
ggbio-1.54.0 Visualization tools for genomic data
ggcyto-1.34.0 Visualize Cytometry data with ggplot
ggdendro-0.2.0 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
ggnewscale-0.5.1 Multiple Fill and Colour Scales in ‘ggplot2’
ggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plot
ggrastr-1.0.2 Rasterize Layers for ‘ggplot2’
ggtangle-0.0.6 Draw Network with Data
ggthemes-5.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’
ggtree-3.14.0 an R package for visualization of tree and annotation data
glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model
graph-1.84.1 graph: A package to handle graph data structures
gsignal-0.3-7 Signal Processing
gson-0.1.0 Base Class and Methods for ‘gson’ Format
gsubfn-0.7 Utilities for Strings and Function Arguments
hapassoc-1.2-9 Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
haplo.stats-1.9.7 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
hardhat-1.4.1 Construct Modeling Packages
hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
hgu133plus2.db 3.13.0 Package Not Found
hopach-2.66.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
hypergate-0.8.5 Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry
igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
illuminaio-0.48.0 Parsing Illumina Microarray Output Files
impute-1.80.0 impute: Imputation for microarray data
inferference-1.0.2 Methods for Causal Inference with Interference
interactiveDisplayBase-1.44.0 Base package for enabling powerful shiny web displays of Bioconductor objects
invgamma-1.1 The Inverse Gamma Distribution
iotools-0.3-5 I/O Tools for Streaming
its-1.1.8 Irregular Time Series
karyoploteR-1.32.0 Plot customizable linear genomes displaying arbitrary data
keyring-1.3.2 Access the System Credential Store from R
kin.cohort-0.7 Analysis of Kin-Cohort Studies
knockoff-0.3.6 The Knockoff Filter for Controlled Variable Selection
kyotil-2024.11-01 Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
latentnet-2.11.0 Latent Position and Cluster Models for Statistical Networks
lgr-0.4.4 A Fully Featured Logging Framework
limma-3.62.2 Linear Models for Microarray and Omics Data
lintr-3.2.0 A ‘Linter’ for R Code
lokern-1.1-12 Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
lpridge-1.1-0 Local Polynomial (Ridge) Regression
lpsymphony-1.34.0 Symphony integer linear programming solver in R
lumi-2.58.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
maSigPro-1.78.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
mapdata-2.3.1 Extra Map Databases
marray-1.84.0 Exploratory analysis for two-color spotted microarray data
metagenomeSeq-1.48.1 Statistical analysis for sparse high-throughput sequencing
methylKit-1.32.1 DNA methylation analysis from high-throughput bisulfite sequencing results
methylumi-2.52.0 Handle Illumina methylation data
minfi-1.52.1 Analyze Illumina Infinium DNA methylation arrays
mixOmics-6.30.0 Omics Data Integration Project
mixsqp-0.3-54 Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
mlapi-0.1.1 Abstract Classes for Building ‘scikit-learn’ Like API
modelenv-0.2.0 Provide Tools to Register Models for Use in ‘tidymodels’
mondate-1.0 Keep Track of Dates in Terms of Months
motifmatchr-1.28.0 Fast Motif Matching in R
msa-1.38.0 Multiple Sequence Alignment
msigdbr-7.5.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
multtest-2.62.0 Resampling-based multiple hypothesis testing
nanotime-0.3.11 Nanosecond-Resolution Time Support for R
ncdfFlow-2.52.1 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
numbers-0.8-5 Number-Theoretic Functions
nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
odbc-1.6.0 Connect to ODBC Compatible Databases (using the DBI Interface)
oligo-1.70.1 Preprocessing tools for oligonucleotide arrays
oligoClasses-1.68.0 Classes for high-throughput arrays supported by oligo and crlmm
openCyto-2.18.0 Hierarchical Gating Pipeline for flow cytometry data
org.Hs.eg.db 3.19.1 Package Not Found
org.Mm.eg.db 3.19.1 Package Not Found
pack-0.1-1 Convert values to/from raw vectors
parsnip-1.3.0 A Common API to Modeling and Analysis Functions
partools-1.1.6 Tools for the ‘Parallel’ Package
pathview-1.46.0 a tool set for pathway based data integration and visualization
paws-0.8.0 Amazon Web Services Software Development Kit
paws.analytics-0.8.0 ‘Amazon Web Services’ Analytics Services
paws.application.integration-0.8.0 ‘Amazon Web Services’ Application Integration Services
paws.common-0.8.2 Paws Low-Level Amazon Web Services API
paws.compute-0.8.0 ‘Amazon Web Services’ Compute Services
paws.cost.management-0.8.0 ‘Amazon Web Services’ Cost Management Services
paws.customer.engagement-0.8.0 ‘Amazon Web Services’ Customer Engagement Services
paws.database-0.8.0 ‘Amazon Web Services’ Database Services
paws.developer.tools-0.8.0 ‘Amazon Web Services’ Developer Tools Services
paws.end.user.computing-0.8.0 ‘Amazon Web Services’ End User Computing Services
paws.machine.learning-0.8.0 ‘Amazon Web Services’ Machine Learning Services
paws.management-0.8.0 ‘Amazon Web Services’ Management & Governance Services
paws.networking-0.8.0 ‘Amazon Web Services’ Networking & Content Delivery Services
paws.security.identity-0.8.0 ‘Amazon Web Services’ Security, Identity, & Compliance Services
paws.storage-0.8.0 ‘Amazon Web Services’ Storage Services
pbs-1.1 Periodic B Splines
pcaMethods-1.98.0 A collection of PCA methods
pdist-1.2.1 Partitioned Distance Function
pedigree-1.4.2 Pedigree Functions
pedigreemm-0.3-5 Pedigree-Based Mixed-Effects Models
perm-1.0-0.4 Exact or Asymptotic Permutation Tests
phyloseq-1.50.0 Handling and analysis of high-throughput microbiome census data
poisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distribution
polyester-1.39.0 Simulate RNA-seq reads
polyreg-0.8.0 Polynomial Regression
poweRlaw-1.0.0 Analysis of Heavy Tailed Distributions
premessa 0.3.4 Package Not Found
preprocessCore-1.68.0 A collection of pre-processing functions
psychotools-0.7-4 Psychometric Modeling Infrastructure
pwalign-1.2.0 Perform pairwise sequence alignments
qdapRegex-0.7.8 Regular Expression Removal, Extraction, and Replacement Tools
qpdf-1.3.4 Split, Combine and Compress PDF Files
qqconf-1.3.2 Creates Simultaneous Testing Bands for QQ-Plots
qtl-1.70 Tools for Analyzing QTL Experiments
quantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimes
quantsmooth-1.72.0 Quantile smoothing and genomic visualization of array data
qvalue-2.38.0 Q-value estimation for false discovery rate control
qvcalc-1.0.4 Quasi Variances for Factor Effects in Statistical Models
r2d3-0.2.6 Interface to ‘D3’ Visualizations
rGADEM-2.54.0 de novo motif discovery
rainbow-3.8 Bagplots, Boxplots and Rainbow Plots for Functional Data
rbenchmark-1.0.0 Benchmarking routine for R
refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from ‘Ensembl’ and ‘UCSC’ Genome Browsers
refund-0.1-37 Regression with Functional Data
regioneR-1.38.0 Association analysis of genomic regions based on permutation tests
regress-1.3-21 Gaussian Linear Models with Linear Covariance Structure
regtools-1.7.0 Regression and Classification Tools
relations-0.6-15 Data Structures and Algorithms for Relations
relevent-1.2-1 Relational Event Models
repr-1.1.7 Serializable Representations
restfulr-0.0.15 R Interface to RESTful Web Services
rgenoud-5.9-0.11 R Version of GENetic Optimization Using Derivatives
rhdf5-2.50.2 R Interface to HDF5
rhdf5filters-1.18.1 HDF5 Compression Filters
rjags-4-16 Bayesian Graphical Models using MCMC
rje-1.12.1 Miscellaneous Useful Functions for Statistics
rslurm-0.6.2 Submit R Calculations to a ‘Slurm’ Cluster
rsparse-0.5.3 Statistical Learning on Sparse Matrices
rstanarm-2.32.1 Bayesian Applied Regression Modeling via Stan
rsvd-1.0.5 Randomized Singular Value Decomposition
rtracklayer-1.66.0 R interface to genome annotation files and the UCSC genome browser
rvcheck-0.2.1 R/Package Version Check
rzmq-0.9.15 R Bindings for ‘ZeroMQ’
samr-3.0 SAM: Significance Analysis of Microarrays
scater-1.34.1 Single-Cell Analysis Toolkit for Gene Expression Data in R
scattermore-1.2 Scatterplots with More Points
schoolmath-0.4.2 Functions and Datasets for Math Used in School
scidb-3.0.0 An R Interface to SciDB
scrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
scuttle-1.16.0 Single-Cell RNA-Seq Analysis Utilities
seqLogo-1.72.0 Sequence logos for DNA sequence alignments
seqminer-9.7 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
sets-1.0-25 Sets, Generalized Sets, Customizable Sets and Intervals
sfd-0.1.0 Space-Filling Design Library
shinyBS-0.61.1 Twitter Bootstrap Components for Shiny
shinyFiles-0.9.3 A Server-Side File System Viewer for Shiny
shinyjqui-0.4.1 ‘jQuery UI’ Interactions and Effects for Shiny
siggenes-1.80.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header Files
snpStats-1.56.0 SnpMatrix and XSnpMatrix classes and methods
sodium-1.4.0 A Modern and Easy-to-Use Crypto Library
sparklyr-1.8.6 R Interface to Apache Spark
sparseMatrixStats-1.18.0 Summary Statistics for Rows and Columns of Sparse Matrices
sparsevctrs-0.3.0 Sparse Vectors for Use in Data Frames
sqldf-0.4-11 Manipulate R Data Frames Using SQL
squash-1.0.9 Color-Based Plots for Multivariate Visualization
srvyr-1.3.0 ‘dplyr’-Like Syntax for Summary Statistics of Survey Data
ssgraph-1.15 Bayesian Graph Structure Learning using Spike-and-Slab Priors
sva-3.54.0 Surrogate Variable Analysis
systemPipeR-2.12.0 systemPipeR: Workflow Environment for Data Analysis and Report Generation
tables-0.9.31 Formula-Driven Table Generation
tergmLite-2.6.1 Fast Simulation of Simple Temporal Exponential Random Graph Models
text2vec-0.6.4 Modern Text Mining Framework for R
tidyposterior-1.0.1 Bayesian Analysis to Compare Models using Resampling Statistics
tilingArray-1.84.0 Transcript mapping with high-density oligonucleotide tiling arrays
timeSeries-4041.111 Financial Time Series Objects (Rmetrics)
tkWidgets-1.84.0 R based tk widgets
treeio-1.30.0 Base Classes and Functions for Phylogenetic Tree Input and Output
tune-1.3.0 Tidy Tuning Tools
txdbmaker-1.2.1 Tools for making TxDb objects from genomic annotations
udunits2-0.13.2.1 Udunits-2 Bindings for R
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uwot-0.2.3 The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
venn-1.12 Draw Venn Diagrams
vimp-2.3.3 Perform Inference on Algorithm-Agnostic Variable Importance
vsn-3.74.0 Variance stabilization and calibration for microarray data
wavethresh-4.7.3 Wavelets Statistics and Transforms
webp-1.3.0 A New Format for Lossless and Lossy Image Compression
widgetTools-1.84.0 Creates an interactive tcltk widget
workflows-1.2.0 Modeling Workflows
workflowsets-1.1.0 Create a Collection of ‘tidymodels’ Workflows
xCell 1.1.0 Package Not Found
xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Tree
yardstick-1.3.2 Tidy Characterizations of Model Performance
yulab.utils-0.2.0 Supporting Functions for Packages Maintained by ‘YuLab-SMU’
zCompositions-1.5.0-4 Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
zigg-0.0.2 Lightweight Interfaces to the ‘Ziggurat’ Pseudo Random Number Generator
zlibbioc-1.52.0 An R packaged zlib-1.2.5
Library List from dependent Modules
ADGofTest-0.3 Anderson-Darling GoF test
AICcmodavg-2.3-3 Model Selection and Multimodel Inference Based on (Q)AIC(c)
ALDEx2-1.38.0 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
ALL 1.48.0 Package Not Found
AMAPVox-2.2.1 LiDAR Data Voxelisation
ANCOMBC-2.8.0 Microbiome differential abudance and correlation analyses with bias correction
ATACseqQC-1.30.0 ATAC-seq Quality Control
AUC-0.3.2 Threshold Independent Performance Measures for Probabilistic Classifiers
AUCell-1.28.0 AUCell: Analysis of ‘gene set’ activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
AgiMicroRna-2.56.0 Processing and Differential Expression Analysis of Agilent microRNA chips
AlgDesign-1.2.1.1 Algorithmic Experimental Design
AnnotationDbi-1.68.0 Manipulation of SQLite-based annotations in Bioconductor
AnnotationFilter-1.30.0 Facilities for Filtering Bioconductor Annotation Resources
AnnotationForge-1.48.0 Tools for building SQLite-based annotation data packages
AnnotationHub-3.14.0 Client to access AnnotationHub resources
BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
BBmisc-1.13 Miscellaneous Helper Functions for B. Bischl
BCEE-1.3.2 The Bayesian Causal Effect Estimation Algorithm
BDgraph-2.73 Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
BH-1.84.0-0 Boost C++ Header Files
BIEN-1.2.6 Tools for Accessing the Botanical Information and Ecology Network Database
BIGL-1.9.3 Biochemically Intuitive Generalized Loewe Model
BMA-3.18.19 Bayesian Model Averaging
BSgenome-1.74.0 Software infrastructure for efficient representation of full genomes and their SNPs
BSgenome.Cfamiliaris.UCSC.canFam3 1.4.0 Package Not Found
BSgenome.Hsapiens.UCSC.hg19 1.4.3 Package Not Found
BSgenome.Hsapiens.UCSC.hg38 1.4.5 Package Not Found
BSgenome.Mmusculus.UCSC.mm10 1.4.3 Package Not Found
BatchJobs-1.9 Batch Computing with R
BayesLogit-2.1 PolyaGamma Sampling
BayesPen-1.0 Bayesian Penalized Credible Regions
BayesianTools-0.1.8 General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
BiasedUrn-2.0.12 Biased Urn Model Distributions
Biobase-2.66.0 Biobase: Base functions for Bioconductor
BiocBaseUtils-1.8.0 General utility functions for developing Bioconductor packages
BiocFileCache-2.14.0 Manage Files Across Sessions
BiocGenerics-0.52.0 S4 generic functions used in Bioconductor
BiocIO-1.16.0 Standard Input and Output for Bioconductor Packages
BiocManager-1.30.25 Access the Bioconductor Project Package Repository
BiocNeighbors-2.0.0 Nearest Neighbor Detection for Bioconductor Packages
BiocParallel-1.40.0 Bioconductor facilities for parallel evaluation
BiocSingular-1.22.0 Singular Value Decomposition for Bioconductor Packages
BiocStyle-2.34.0 Standard styles for vignettes and other Bioconductor documents
BiocVersion-3.20.0 Set the appropriate version of Bioconductor packages
Biostrings-2.74.0 Efficient manipulation of biological strings
Boruta-8.0.0 Wrapper Algorithm for All Relevant Feature Selection
Brobdingnag-1.2-9 Very Large Numbers in R
CAGEfightR-1.26.0 Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
CAGEr-2.12.0 Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
CAMERA-1.62.0 Collection of annotation related methods for mass spectrometry data
CBPS-0.23 Covariate Balancing Propensity Score
CGHbase-1.66.0 CGHbase: Base functions and classes for arrayCGH data analysis.
CGHcall-2.68.0 Calling aberrations for array CGH tumor profiles.
CNEr-1.42.0 CNE Detection and Visualization
CVST-0.2-3 Fast Cross-Validation via Sequential Testing
CVXR-1.0-15 Disciplined Convex Optimization
Cairo-1.6-2 R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output
Category-2.72.0 Category Analysis
ChIPpeakAnno-3.40.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
ChIPseeker-1.42.0 ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ComICS-1.0.4 Computational Methods for Immune Cell-Type Subsets
CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
ComplexHeatmap-2.22.0 Make Complex Heatmaps
ComplexUpset-1.3.3 Create Complex UpSet Plots Using ‘ggplot2’ Components
ConsRank-2.1.4 Compute the Median Ranking(s) According to the Kemeny’s Axiomatic Approach
ConsensusClusterPlus-1.70.0 ConsensusClusterPlus
CovSel-1.2.1 Model-Free Covariate Selection
CytoML-2.18.0 A GatingML Interface for Cross Platform Cytometry Data Sharing
DBI-1.2.3 R Database Interface
DECIPHER-3.2.0 Tools for curating, analyzing, and manipulating biological sequences
DEGseq-1.60.0 Identify Differentially Expressed Genes from RNA-seq data
DESeq2-1.46.0 Differential gene expression analysis based on the negative binomial distribution
DEoptim-2.2-8 Global Optimization by Differential Evolution
DEoptimR-1.1-3-1 Differential Evolution Optimization in Pure R
DHARMa-0.4.7 Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
DMCfun-4.0.1 Diffusion Model of Conflict (DMC) in Reaction Time Tasks
DNABarcodes-1.36.0 A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
DNAcopy-1.80.0 DNA Copy Number Data Analysis
DO.db 2.9 Package Not Found
DOSE-4.0.0 Disease Ontology Semantic and Enrichment analysis
DRIMSeq-1.34.0 Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
DRR-0.0.4 Dimensionality Reduction via Regression
DSS-2.54.0 Dispersion shrinkage for sequencing data
DT-0.33 A Wrapper of the JavaScript Library ‘DataTables’
DTRreg-2.2 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
DataCombine-0.2.21 Tools for Easily Combining and Cleaning Data Sets
DeconRNASeq-1.48.0 Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
DelayedArray-0.32.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
DelayedMatrixStats-1.28.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
DepthProc-2.1.5 Statistical Depth Functions for Multivariate Analysis
Deriv-4.1.6 Symbolic Differentiation
DescTools-0.99.58 Tools for Descriptive Statistics
DiagrammeR-1.0.11 Graph/Network Visualization
DiceKriging-1.6.0 Kriging Methods for Computer Experiments
DirichletMultinomial-1.48.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
DistributionUtils-0.6-1 Distribution Utilities
DropletUtils-1.26.0 Utilities for Handling Single-Cell Droplet Data
DynDoc-1.84.0 Dynamic document tools
EBImage-4.48.0 Image processing and analysis toolbox for R
ECOSolveR-0.5.5 Embedded Conic Solver in R
ENMeval-2.0.4 Automated Tuning and Evaluations of Ecological Niche Models
EValue-4.1.3 Sensitivity Analyses for Unmeasured Confounding and Other Biases in Observational Studies and Meta-Analyses
EasyABC-1.5.2 Efficient Approximate Bayesian Computation Sampling Schemes
EnsDb.Hsapiens.v75 2.99.0 Package Not Found
EnsDb.Hsapiens.v79 2.99.0 Package Not Found
EnsDb.Hsapiens.v86 2.99.0 Package Not Found
EnvStats-3.0.0 Package for Environmental Statistics, Including US EPA Guidance
ExPosition-2.8.23 Exploratory Analysis with the Singular Value Decomposition
Exact-3.3 Unconditional Exact Test
ExperimentHub-2.14.0 Client to access ExperimentHub resources
FDb.InfiniumMethylation.hg19 2.2.0 Package Not Found
FKSUM-1.0.1 Fast Kernel Sums
FME-1.3.6.3 A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis
FNN-1.1.4.1 Fast Nearest Neighbor Search Algorithms and Applications
FRASER-2.2.0 Find RAre Splicing Events in RNA-Seq Data
FactoMineR-2.11 Multivariate Exploratory Data Analysis and Data Mining
FactorCopula-0.9.3 Factor, Bi-Factor, Second-Order and Factor Tree Copula Models
FlowSOM-2.14.0 Using self-organizing maps for visualization and interpretation of cytometry data
FlowSorted.Blood.EPIC 2.10.0 Package Not Found
FlowSorted.CordBloodCombined.450k 1.22.0 Package Not Found
Formula-1.2-5 Extended Model Formulas
GENESIS-2.36.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GENIE3-1.28.0 GEne Network Inference with Ensemble of trees
GEOmap-2.5-11 Topographic and Geologic Mapping
GEOquery-2.74.0 Get data from NCBI Gene Expression Omnibus (GEO)
GGally-2.2.1 Extension to ‘ggplot2’
GJRM-0.2-6.7 Generalised Joint Regression Modelling
GLAD-2.70.0 Gain and Loss Analysis of DNA
GO.db 3.20.0 Package Not Found
GOSemSim-2.32.0 GO-terms Semantic Similarity Measures
GOstats-2.72.0 Tools for manipulating GO and microarrays
GPArotation-2024.3-1 Gradient Projection Factor Rotation
GSA-1.03.3 Gene Set Analysis
GSEABase-1.68.0 Gene set enrichment data structures and methods
GSVA-2.0.1 Gene Set Variation Analysis for Microarray and RNA-Seq Data
GUTS-1.2.5 Fast Calculation of the Likelihood of a Stochastic Survival Model
GWASExactHW-1.2 Exact Hardy-Weinburg Testing for Genome Wide Association Studies
GWASTools-1.52.0 Tools for Genome Wide Association Studies
GenSA-1.1.14.1 R Functions for Generalized Simulated Annealing
GeneNet-1.2.16 Modeling and Inferring Gene Networks
GenomeInfoDb-1.42.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
GenomeInfoDbData 1.2.13 Package Not Found
GenomicAlignments-1.42.0 Representation and manipulation of short genomic alignments
GenomicFeatures-1.58.0 Query the gene models of a given organism/assembly
GenomicFiles-1.42.0 Distributed computing by file or by range
GenomicInteractions-1.40.0 Utilities for handling genomic interaction data
GenomicRanges-1.58.0 Representation and manipulation of genomic intervals
GenomicScores-2.18.0 Infrastructure to work with genomewide position-specific scores
GetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable Interpolation
GillespieSSA-0.6.2 Gillespie’s Stochastic Simulation Algorithm (SSA)
Glimma-2.16.0 Interactive visualizations for gene expression analysis
GlobalAncova-4.24.0 Global test for groups of variables via model comparisons
GlobalOptions-0.1.2 Generate Functions to Get or Set Global Options
Gviz-1.50.0 Plotting data and annotation information along genomic coordinates
GxEScanR-2.0.2 Run GWAS/GWEIS Scans Using Binary Dosage Files
HDF5Array-1.34.0 HDF5 datasets as array-like objects in R
HDO.db 1.0.0 Package Not Found
HGNChelper-0.8.15 Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols
HMMcopy-1.48.0 Copy number prediction with correction for GC and mappability bias for HTS data
HWxtest-1.1.9 Exact Tests for Hardy-Weinberg Proportions
HiCBricks-1.24.0 Framework for Storing and Accessing Hi-C Data Through HDF Files
HiCcompare-1.28.0 HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
HiddenMarkov-1.8-13 Hidden Markov Models
Hmisc-5.2-0 Harrell Miscellaneous
Hmsc-3.0-13 Hierarchical Model of Species Communities
Homo.sapiens 1.3.1 Package Not Found
IDPmisc-1.1.21 ‘Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)’
IHW-1.34.0 Independent Hypothesis Weighting
IRanges-2.40.0 Foundation of integer range manipulation in Bioconductor
ISOcodes-2024.02.12 Selected ISO Codes
ISOweek-0.6-2 Week of the year and weekday according to ISO 8601
IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.1 Package Not Found
IlluminaHumanMethylation450kmanifest 0.4.0 Package Not Found
IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0 Package Not Found
IlluminaHumanMethylationEPICanno.ilm10b4.hg19 0.6.0 Package Not Found
IlluminaHumanMethylationEPICmanifest 0.3.0 Package Not Found
IlluminaHumanMethylationEPICv2anno.20a1.hg38 1.0.0 Package Not Found
IlluminaHumanMethylationEPICv2manifest 1.0.0 Package Not Found
InteractionSet-1.34.0 Base Classes for Storing Genomic Interaction Data
Iso-0.0-21 Functions to Perform Isotonic Regression
JADE-2.0-4 Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria
JASPAR2020 0.99.10 Package Not Found
JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J. Buttlar
KEGGREST-1.46.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
KEGGgraph-1.66.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KODAMA-2.4.1 Knowledge Discovery by Accuracy Maximization
KernSmooth-2.23-24 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
LCFdata-2.0 Data sets for package “LMERConvenienceFunctions”
LEA-3.18.0 LEA: an R package for Landscape and Ecological Association Studies
LMERConvenienceFunctions-3.0 Model Selection and Post-Hoc Analysis for (G)LMER Models
LaplacesDemon-16.1.6 Complete Environment for Bayesian Inference
LearnBayes-2.15.1 Functions for Learning Bayesian Inference
Lmoments-1.3-1 L-Moments and Quantile Mixtures
M3Drop-1.32.0 Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
MALDIquant-1.22.3 Quantitative Analysis of Mass Spectrometry Data
MASS-7.3-61 Support Functions and Datasets for Venables and Ripley’s MASS
MBA-0.1-2 Multilevel B-Spline Approximation
MCMCpack-1.7-1 Markov Chain Monte Carlo (MCMC) Package
MEDIPS-1.58.0 DNA IP-seq data analysis
MESS-0.5.12 Miscellaneous Esoteric Statistical Scripts
MIIVsem-0.5.8 Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
MLInterfaces-1.86.0 Uniform interfaces to R machine learning procedures for data in Bioconductor containers
MLmetrics-1.1.3 Machine Learning Evaluation Metrics
MSnbase-2.32.0 Base Functions and Classes for Mass Spectrometry and Proteomics
MSstats-4.14.0 Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
MSstatsConvert-1.16.0 Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
MSstatsLiP-1.12.0 LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
MSstatsPTM-2.8.1 Statistical Characterization of Post-translational Modifications
MSstatsTMT-2.14.1 Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
MassSpecWavelet-1.72.0 Peak Detection for Mass Spectrometry data using wavelet-based algorithms
MatchIt-4.6.0 Nonparametric Preprocessing for Parametric Causal Inference
Matching-4.10-15 Multivariate and Propensity Score Matching with Balance Optimization
Matrix-1.7-1 Sparse and Dense Matrix Classes and Methods
MatrixGenerics-1.18.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
MatrixModels-0.5-3 Modelling with Sparse and Dense Matrices
MetaUtility-2.1.2 Utility Functions for Conducting and Interpreting Meta-Analyses
MetaboCoreUtils-1.14.0 Core Utils for Metabolomics Data
MethylSeekR-1.46.0 Segmentation of Bis-seq data
Mfuzz-2.66.0 Soft clustering of omics time series data
ModelMetrics-1.2.2.2 Rapid Calculation of Model Metrics
MonteCarlo-1.0.6 Automatic Parallelized Monte Carlo Simulations
MotifDb-1.48.0 An Annotated Collection of Protein-DNA Binding Sequence Motifs
MsCoreUtils-1.18.0 Core Utils for Mass Spectrometry Data
MsExperiment-1.8.0 Infrastructure for Mass Spectrometry Experiments
MsFeatures-1.14.0 Functionality for Mass Spectrometry Features
MultiAssayExperiment-1.32.0 Software for the integration of multi-omics experiments in Bioconductor
MultiDataSet-1.34.0 Implementation of MultiDataSet and ResultSet
NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
NCmisc-1.2.0 Miscellaneous Functions for Creating Adaptive Functions and Scripts
NISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NIST
NLP-0.3-2 Natural Language Processing Infrastructure
NMF-0.28 Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
NOISeq-2.50.0 Exploratory analysis and differential expression for RNA-seq data
OUTRIDER-1.24.0 OUTRIDER - OUTlier in RNA-Seq fInDER
OceanView-1.0.7 Visualisation of Oceanographic Data and Model Output
OpenMx-2.21.13 Extended Structural Equation Modelling
OrganismDbi-1.48.0 Software to enable the smooth interfacing of different database packages
PCAmatchR-0.3.3 Match Cases to Controls Based on Genotype Principal Components
PFAM.db 3.20.0 Package Not Found
PKI-0.1-14 Public Key Infrastucture for R Based on the X.509 Standard
PMA-1.2-4 Penalized Multivariate Analysis
PRROC-1.3.1 Precision-Recall and ROC Curves for Weighted and Unweighted Data
PSCBS-0.67.0 Analysis of Parent-Specific DNA Copy Numbers
PSMatch-1.10.0 Handling and Managing Peptide Spectrum Matches
PWEALL-1.3.0.1 Design and Monitoring of Survival Trials Accounting for Complex Situations
ParamHelpers-1.14.1 Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
PearsonDS-1.3.1 Pearson Distribution System
PermAlgo-1.2 Permutational Algorithm to Simulate Survival Data
PoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log linear model
Polychrome-1.5.1 Qualitative Palettes with Many Colors
PresenceAbsence-1.1.11 Presence-Absence Model Evaluation
ProtGenerics-1.38.0 Generic infrastructure for Bioconductor mass spectrometry packages
Publish-2023.01.17 Format Output of Various Routines in a Suitable Way for Reports and Publication
PureCN-2.12.0 Copy number calling and SNV classification using targeted short read sequencing
QDNAseq-1.42.0 Quantitative DNA Sequencing for Chromosomal Aberrations
QFeatures-1.16.0 Quantitative features for mass spectrometry data
QuickJSR-1.4.0 Interface for the ‘QuickJS’ Lightweight ‘JavaScript’ Engine
R.cache-0.16.0 Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations
R.devices-2.17.2 Unified Handling of Graphics Devices
R.filesets-2.15.1 Easy Handling of and Access to Files Organized in Structured Directories
R.huge-0.10.1 Methods for Accessing Huge Amounts of Data [deprecated]
R.matlab-3.7.0 Read and Write MAT Files and Call MATLAB from Within R
R.methodsS3-1.8.2 S3 Methods Simplified
R.oo-1.27.0 R Object-Oriented Programming with or without References
R.rsp-0.46.0 Dynamic Generation of Scientific Reports
R.utils-2.12.3 Various Programming Utilities
R2WinBUGS-2.1-22.1 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
R6-2.5.1 Encapsulated Classes with Reference Semantics
RANN-2.6.2 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
RBGL-1.82.0 An interface to the BOOST graph library
RBesT-1.7-4 R Bayesian Evidence Synthesis Tools
RCAL-2.0 Regularized Calibrated Estimation
RCircos-1.2.2 Circos 2D Track Plot
RColorBrewer-1.1-3 ColorBrewer Palettes
RCurl-1.98-1.16 General Network (HTTP/FTP/…) Client Interface for R
RFOC-3.4-10 Graphics for Spherical Distributions and Earthquake Focal Mechanisms
RGCCA-3.0.3 Regularized and Sparse Generalized Canonical Correlation Analysis for Multiblock Data
RInside-0.2.18 C++ Classes to Embed R in C++ (and C) Applications
RItools-0.3-4 Randomization Inference Tools
RJSONIO-1.3-1.9 Serialize R Objects to JSON, JavaScript Object Notation
RMTstat-0.3.1 Distributions, Statistics and Tests Derived from Random Matrix Theory
RNASeqPower-1.46.0 Sample size for RNAseq studies
RNeXML-2.4.11 Semantically Rich I/O for the ‘NeXML’ Format
RNifti-1.7.0 Fast R and C++ Access to NIfTI Images
ROC-1.82.0 utilities for ROC, with microarray focus
ROCR-1.0-11 Visualizing the Performance of Scoring Classifiers
ROI-1.0-1 R Optimization Infrastructure
ROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’
ROntoTools-2.34.0 R Onto-Tools suite
RPMG-2.2-7 Graphical User Interface (GUI) for Interactive R Analysis Sessions
RPMM-1.25 Recursively Partitioned Mixture Model
RPostgreSQL-0.7-7 R Interface to the ‘PostgreSQL’ Database System
RProtoBufLib-2.18.0 C++ headers and static libraries of Protocol buffers
RPushbullet-0.3.4 R Interface to the Pushbullet Messaging Service
RSEIS-4.2-4 Seismic Time Series Analysis Tools
RSNNS-0.4-17 Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
RSQLite-2.3.8 SQLite Interface for R
RSpectra-0.16-2 Solvers for Large-Scale Eigenvalue and SVD Problems
RUnit-0.4.33 R Unit Test Framework
RWeka-0.4-46 R/Weka Interface
RWekajars-3.9.3-2 R/Weka Interface Jars
Rborist-0.3-7 Extensible, Parallelizable Implementation of the Random Forest Algorithm
Rcgmin-2022-4.30 Conjugate Gradient Minimization of Nonlinear Functions with Box Constraints
RcisTarget-1.26.0 RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
Rcpp-1.0.13-1 Seamless R and C++ Integration
RcppAnnoy-0.0.22 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest Neighbors
RcppArmadillo-14.2.0-1 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library
RcppEigen-0.3.4.0.2 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra Library
RcppGSL-0.3.13 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and Matrices
RcppHNSW-0.6.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest Neighbors
RcppML-0.3.7 Rcpp Machine Learning Library
RcppParallel-5.1.9 Parallel Programming Tools for ‘Rcpp’
RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R Packages
RcppRoll-0.3.1 Efficient Rolling / Windowed Operations
RcppTOML-0.2.2 ‘Rcpp’ Bindings to Parser for “Tom’s Obvious Markup Language”
RcppThread-2.1.7 R-Friendly Threading in C++
RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG Implementations
Rdpack-2.6.2 Update and Manipulate Rd Documentation Objects
ReactomePA-1.50.0 Reactome Pathway Analysis
RefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Repitools-1.52.0 Epigenomic tools
ReportingTools-2.46.0 Tools for making reports in various formats
ResidualMatrix-1.16.0 Creating a DelayedMatrix of Regression Residuals
Rfast-2.1.0 A Collection of Efficient and Extremely Fast R Functions
Rglpk-0.6-5.1 R/GNU Linear Programming Kit Interface
Rgraphviz-2.50.0 Provides plotting capabilities for R graph objects
Rhdf5lib-1.28.0 hdf5 library as an R package
RhpcBLASctl-0.23-42 Control the Number of Threads on ‘BLAS’
Rhtslib-3.2.0 HTSlib high-throughput sequencing library as an R package
Rmpfr-1.0-0 Interface R to MPFR - Multiple Precision Floating-Point Reliable
RnBeads-2.24.0 RnBeads
RnBeads.hg19 1.38.0 Package Not Found
RnBeads.hg38 1.38.0 Package Not Found
RnBeads.mm10 2.14.0 Package Not Found
RnBeads.mm9 1.38.0 Package Not Found
RnBeads.rn5 1.38.0 Package Not Found
Rook-1.2 HTTP Web Server for R
Rsamtools-2.22.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Rserve-1.8-13 Versatile R Server
Rsolnp-1.16 General Non-Linear Optimization
Rssa-1.1 A Collection of Methods for Singular Spectrum Analysis
Rsubread-2.20.0 Mapping, quantification and variant analysis of sequencing data
Rtsne-0.17 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
Rttf2pt1-1.3.12 ‘ttf2pt1’ Program
Rvmmin-2018-4.17.1 Variable Metric Nonlinear Function Minimization
Rwave-2.6-5 Time-Frequency Analysis of 1-D Signals
S4Arrays-1.6.0 Foundation of array-like containers in Bioconductor
S4Vectors-0.44.0 Foundation of vector-like and list-like containers in Bioconductor
SBdecomp-1.2 Estimation of the Proportion of SB Explained by Confounders
SC3-1.34.0 Single-Cell Consensus Clustering
SCANVIS-1.20.0 SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
SDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
SKAT-2.2.5 SNP-Set (Sequence) Kernel Association Test
SMVar-1.3.4 Structural Model for Variances
SNFtool-2.3.1 Similarity Network Fusion
SNPRelate-1.40.0 Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
SOAR-0.99-11 Memory management in R by delayed assignments
SPAtest-3.1.2 Score Test and Meta-Analysis Based on Saddlepoint Approximation
SPIA-2.58.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
SPOTlight-1.10.0 SPOTlight: Spatial Transcriptomics Deconvolution
SQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
SamSPECTRAL-1.60.0 Identifies cell population in flow cytometry data
ScaledMatrix-1.14.0 Creating a DelayedMatrix of Scaled and Centered Values
SeqArray-1.46.0 Data Management of Large-Scale Whole-Genome Sequence Variant Calls
SeqVarTools-1.44.0 Tools for variant data
Seurat-5.1.0 Tools for Single Cell Genomics
SeuratObject-5.0.2 Data Structures for Single Cell Data
ShortRead-1.64.0 FASTQ input and manipulation
Signac-1.14.0 Analysis of Single-Cell Chromatin Data
SignifReg-4.3 Consistent Significance Controlled Variable Selection in Generalized Linear Regression
SimBu-1.8.0 Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
SimDesign-2.17.1 Structure for Organizing Monte Carlo Simulation Designs
SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
SingleCellExperiment-1.28.1 S4 Classes for Single Cell Data
SingleR-2.8.0 Reference-Based Single-Cell RNA-Seq Annotation
SnowballC-0.7.1 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 Library
SparseArray-1.6.0 High-performance sparse data representation and manipulation in R
SparseM-1.84-2 Sparse Linear Algebra
SpatialExperiment-1.16.0 S4 Class for Spatially Resolved -omics Data
Spectra-1.16.0 Spectra Infrastructure for Mass Spectrometry Data
StanHeaders-2.32.10 C++ Header Files for Stan
StatMatch-1.4.2 Statistical Matching or Data Fusion
SummarizedExperiment-1.36.0 A container (S4 class) for matrix-like assays
SuperLearner-2.0-29 Super Learner Prediction
SuppDists-1.1-9.8 Supplementary Distributions
TFBSTools-1.44.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
TFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight Matrices
TFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination Method
TH.data-1.1-2 TH’s Data Archive
TMB-1.9.15 Template Model Builder: A General Random Effect Tool Inspired by ‘ADMB’
TSP-1.2-4 Traveling Salesperson Problem (TSP)
TTR-0.24.4 Technical Trading Rules
TailRank-3.2.2 The Tail-Rank Statistic
TeachingDemos-2.13 Demonstrations for Teaching and Learning
TraMineR-2.2-10 Trajectory Miner: a Sequence Analysis Toolkit
TrajectoryUtils-1.14.0 Single-Cell Trajectory Analysis Utilities
TreeSummarizedExperiment-2.14.0 TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
TruncatedNormal-2.3 Truncated Multivariate Normal and Student Distributions
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 Package Not Found
TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0 Package Not Found
UCSC.utils-1.2.0 Low-level utilities to retrieve data from the UCSC Genome Browser
UCell-2.10.1 Rank-based signature enrichment analysis for single-cell data
UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
V8-6.0.0 Embedded JavaScript and WebAssembly Engine for R
VGAM-1.1-12 Vector Generalized Linear and Additive Models
VIM-6.2.2 Visualization and Imputation of Missing Values
VSURF-1.2.0 Variable Selection Using Random Forests
VariantAnnotation-1.52.0 Annotation of Genetic Variants
VennDiagram-1.7.3 Generate High-Resolution Venn and Euler Plots
VineCopula-2.5.1 Statistical Inference of Vine Copulas
WGCNA-1.73 Weighted Correlation Network Analysis
WeightSVM-1.7-16 Subject Weighted Support Vector Machines
WikidataQueryServiceR-1.0.0 API Client Library for ‘Wikidata Query Service’
WikidataR-2.3.3 Read-Write API Client Library for Wikidata
WikipediR-1.7.1 A MediaWiki API Wrapper
Wrench-1.24.0 Wrench normalization for sparse count data
WriteXLS-6.7.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files
XBRL-0.99.19.1 Extraction of Business Financial Information from ‘XBRL’ Documents
XML-3.99-0.17 Tools for Parsing and Generating XML Within R and S-Plus
XVector-0.46.0 Foundation of external vector representation and manipulation in Bioconductor
abc-2.2.1 Tools for Approximate Bayesian Computation (ABC)
abc.data-1.1 Data Only: Tools for Approximate Bayesian Computation (ABC)
abe-3.0.1 Augmented Backward Elimination
abind-1.4-8 Combine Multidimensional Arrays
acepack-1.4.2 ACE and AVAS for Selecting Multiple Regression Transformations
adabag-5.0 Applies Multiclass AdaBoost.M1, SAMME and Bagging
ade4-1.7-22 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
admisc-0.36 Adrian Dusa’s Miscellaneous
affxparser-1.78.0 Affymetrix File Parsing SDK
affy-1.84.0 Methods for Affymetrix Oligonucleotide Arrays
affycoretools-1.78.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
affyio-1.76.0 Tools for parsing Affymetrix data files
aggregation-1.0.1 p-Value Aggregation Methods
agricolae-1.3-7 Statistical Procedures for Agricultural Research
akima-0.6-3.4 Interpolation of Irregularly and Regularly Spaced Data
alabama-2023.1.0 Constrained Nonlinear Optimization
alluvial-0.1-2 Alluvial Diagrams
animation-2.7 A Gallery of Animations in Statistics and Utilities to Create Animations
annaffy-1.78.0 Annotation tools for Affymetrix biological metadata
annotate-1.84.0 Annotation for microarrays
anytime-0.3.9 Anything to ‘POSIXct’ or ‘Date’ Converter
aod-1.3.3 Analysis of Overdispersed Data
apcluster-1.4.13 Affinity Propagation Clustering
ape-5.8 Analyses of Phylogenetics and Evolution
aplot-0.2.3 Decorate a ‘ggplot’ with Associated Information
argparse-2.2.4 Command Line Optional and Positional Argument Parser
aricode-1.0.3 Efficient Computations of Standard Clustering Comparison Measures
arm-1.14-4 Data Analysis Using Regression and Multilevel/Hierarchical Models
aroma.affymetrix-3.2.2 Analysis of Large Affymetrix Microarray Data Sets
aroma.apd-0.7.0 A Probe-Level Data File Format Used by ‘aroma.affymetrix’ [deprecated]
aroma.core-3.3.1 Core Methods and Classes Used by ‘aroma.*’ Packages Part of the Aroma Framework
aroma.light-3.36.0 Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
arrayhelpers-1.1-0 Convenience Functions for Arrays
ash-1.0-15 David Scott’s ASH Routines
askpass-1.2.1 Password Entry Utilities for R, Git, and SSH
asnipe-1.1.17 Animal Social Network Inference and Permutations for Ecologists
assertive-0.3-6 Readable Check Functions to Ensure Code Integrity
assertive.base-0.0-9 A Lightweight Core of the ‘assertive’ Package
assertive.code-0.0-4 Assertions to Check Properties of Code
assertive.data-0.0-3 Assertions to Check Properties of Data
assertive.data.uk-0.0-2 Assertions to Check Properties of Strings
assertive.data.us-0.0-2 Assertions to Check Properties of Strings
assertive.datetimes-0.0-3 Assertions to Check Properties of Dates and Times
assertive.files-0.0-2 Assertions to Check Properties of Files
assertive.matrices-0.0-2 Assertions to Check Properties of Matrices
assertive.models-0.0-2 Assertions to Check Properties of Models
assertive.numbers-0.0-2 Assertions to Check Properties of Numbers
assertive.properties-0.0-5 Assertions to Check Properties of Variables
assertive.reflection-0.0-5 Assertions for Checking the State of R
assertive.sets-0.0-3 Assertions to Check Properties of Sets
assertive.strings-0.0-3 Assertions to Check Properties of Strings
assertive.types-0.0-3 Assertions to Check Types of Variables
assertthat-0.2.1 Easy Pre and Post Assertions
assorthead-1.0.0 Assorted Header-Only C++ Libraries
audio-0.1-11 Audio Interface for R
aws-2.5-6 Adaptive Weights Smoothing
aws.s3-0.3.21 ‘AWS S3’ Client Package
aws.signature-0.6.0 Amazon Web Services Request Signatures
awsMethods-1.1-1 Class and Methods Definitions for Packages ‘aws’, ‘adimpro’, ‘fmri’, ‘dwi’
babelgene-22.9 Gene Orthologs for Model Organisms in a Tidy Data Format
backports-1.5.0 Reimplementations of Functions Introduced Since R-3.0.0
bacr-1.0.1 Bayesian Adjustment for Confounding
ballgown-2.38.0 Flexible, isoform-level differential expression analysis
bartMachine-1.3.4.1 Bayesian Additive Regression Trees
bartMachineJARs-1.2.1 bartMachine JARs
base built in
base64-2.0.2 Base64 Encoder and Decoder
base64enc-0.1-3 Tools for base64 encoding
basilisk-1.18.0 Freezing Python Dependencies Inside Bioconductor Packages
basilisk.utils-1.18.0 Basilisk Installation Utilities
batchelor-1.22.0 Single-Cell Batch Correction Methods
batchmeans-1.0-4 Consistent Batch Means Estimation of Monte Carlo Standard Errors
baySeq-2.40.0 Empirical Bayesian analysis of patterns of differential expression in count data
bayesm-3.1-6 Bayesian Inference for Marketing/Micro-Econometrics
bayesplot-1.11.1 Plotting for Bayesian Models
bayestestR-0.15.0 Understand and Describe Bayesian Models and Posterior Distributions
bbmle-1.0.25.1 Tools for General Maximum Likelihood Estimation
bdsmatrix-1.3-7 Routines for Block Diagonal Symmetric Matrices
beachmat-2.22.0 Compiling Bioconductor to Handle Each Matrix Type
beanplot-1.3.1 Visualization via Beanplots (Like Boxplot/Stripchart/Violin Plot)
beepr-2.0 Easily Play Notification Sounds on any Platform
beeswarm-0.4.0 The Bee Swarm Plot, an Alternative to Stripchart
berryFunctions-1.22.5 Function Collection Related to Plotting and Hydrology
betareg-3.2-1 Beta Regression
bibtex-0.5.1 Bibtex Parser
bigD-0.3.0 Flexibly Format Dates and Times to a Given Locale
bigmemory-4.6.4 Manage Massive Matrices with Shared Memory and Memory-Mapped Files
bigmemory.sri-0.1.8 A Shared Resource Interface for Bigmemory Project Packages
bindr-0.1.2 Parametrized Active Bindings
bindrcpp-0.2.3 An ‘Rcpp’ Interface to Active Bindings
bio3d-2.4-5 Biological Structure Analysis
biom-0.3.12 An interface package (beta) for the BIOM file format.
biomaRt-2.62.0 Interface to BioMart databases (i.e. Ensembl)
biomformat-1.34.0 An interface package for the BIOM file format
biomod2-4.2-5-2 Ensemble Platform for Species Distribution Modeling
biovizBase-1.54.0 Basic graphic utilities for visualization of genomic data.
bit-4.5.0 Classes and Methods for Fast Memory-Efficient Boolean Selections
bit64-4.5.2 A S3 Class for Vectors of 64bit Integers
bitops-1.0-9 Bitwise Operations
blavaan-0.5-6 Bayesian Latent Variable Analysis
blme-1.0-6 Bayesian Linear Mixed-Effects Models
blob-1.2.4 A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’)
bluster-1.16.0 Clustering Algorithms for Bioconductor
bmp-0.3 Read Windows Bitmap (BMP) Images
bnlearn-5.0.1 Bayesian Network Structure Learning, Parameter Learning and Inference
bold-1.3.0 Interface to Bold Systems API
bookdown-0.41 Authoring Books and Technical Documents with R Markdown
boot-1.3-31 Bootstrap Functions (Originally by Angelo Canty for S)
bootstrap-2019.6 Functions for the Book “An Introduction to the Bootstrap”
brew-1.0-10 Templating Framework for Report Generation
brglm-0.7.2 Bias Reduction in Binomial-Response Generalized Linear Models
bridgedist-0.1.3 An Implementation of the Bridge Distribution with Logit-Link as in Wang and Louis (2003)
bridgesampling-1.1-2 Bridge Sampling for Marginal Likelihoods and Bayes Factors
brio-1.1.5 Basic R Input Output
brms-2.22.0 Bayesian Regression Models using ‘Stan’
broom-1.0.7 Convert Statistical Objects into Tidy Tibbles
broom.helpers-1.17.0 Helpers for Model Coefficients Tibbles
broom.mixed-0.2.9.6 Tidying Methods for Mixed Models
bslib-0.8.0 Custom ‘Bootstrap’ ‘Sass’ Themes for ‘shiny’ and ‘rmarkdown’
bsseq-1.42.0 Analyze, manage and store whole-genome methylation data
bst-0.3-24 Gradient Boosting
bumphunter-1.48.0 Bump Hunter
cNORM-3.4.0 Continuous Norming
cSEM-0.5.0 Composite-Based Structural Equation Modeling
ca-0.71.1 Simple, Multiple and Joint Correspondence Analysis
caTools-1.18.3 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
cachem-1.1.0 Cache R Objects with Automatic Pruning
calibrate-1.7.7 Calibration of Scatterplot and Biplot Axes
callr-3.7.6 Call R from R
car-3.1-3 Companion to Applied Regression
carData-3.0-5 Companion to Applied Regression Data Sets
cards-0.3.0 Analysis Results Data
caret-6.0-94 Classification and Regression Training
catlearn-1.0 Formal Psychological Models of Categorization and Learning
ccdata 1.32.0 Package Not Found
ccmap-1.32.0 Combination Connectivity Mapping
celestial-1.4.6 Collection of Common Astronomical Conversion Routines and Functions
cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
cgdsr-1.3.0 R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)
cghFLasso-0.2-1 Detecting hot spot on CGH array data with fused lasso<U+000a>regression.
changepoint-2.3 Methods for Changepoint Detection
checkmate-2.3.2 Fast and Versatile Argument Checks
chemometrics-1.4.4 Multivariate Statistical Analysis in Chemometrics
chk-0.9.2 Check User-Supplied Function Arguments
chkptstanr-0.1.1 Checkpoint MCMC Sampling with ‘Stan’
chromVAR-1.28.0 Chromatin Variation Across Regions
chron-2.3-61 Chronological Objects which Can Handle Dates and Times
circlize-0.4.16 Circular Visualization
circular-0.5-1 Circular Statistics
clValid-0.7 Validation of Clustering Results
class-7.3-22 Functions for Classification
classInt-0.4-10 Choose Univariate Class Intervals
cld2-1.2.5 Google’s Compact Language Detector 2
cli-3.6.3 Helpers for Developing Command Line Interfaces
clipr-0.8.0 Read and Write from the System Clipboard
clisymbols-1.2.0 Unicode Symbols at the R Prompt
clock-0.7.1 Date-Time Types and Tools
clue-0.3-66 Cluster Ensembles
cluster-2.1.6 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al.
clusterGeneration-1.3.8 Random Cluster Generation (with Specified Degree of Separation)
clusterProfiler-4.14.3 A universal enrichment tool for interpreting omics data
clusterRepro-0.9 Reproducibility of Gene Expression Clusters
clustree-0.5.1 Visualise Clusterings at Different Resolutions
cmna-1.0.5 Computational Methods for Numerical Analysis
cmprsk-2.2-12 Subdistribution Analysis of Competing Risks
cobalt-4.5.5 Covariate Balance Tables and Plots
cobs-1.3-8 Constrained B-Splines (Sparse Matrix Based)
coda-0.19-4.1 Output Analysis and Diagnostics for MCMC
codetools-0.2-20 Code Analysis Tools for R
coin-1.4-3 Conditional Inference Procedures in a Permutation Test Framework
collapse-2.0.18 Advanced and Fast Data Transformation
coloc-5.2.3 Colocalisation Tests of Two Genetic Traits
colorRamps-2.3.4 Builds Color Tables
colorspace-2.1-1 A Toolbox for Manipulating and Assessing Colors and Palettes
colourpicker-1.3.0 A Colour Picker Tool for Shiny and for Selecting Colours in Plots
combinat-0.0-8 combinatorics utilities
commonmark-1.9.2 High Performance CommonMark and Github Markdown Rendering in R
compiler built in
compositions-2.0-8 Compositional Data Analysis
conditionz-0.1.0 Control How Many Times Conditions are Thrown
conflicted-1.2.0 An Alternative Conflict Resolution Strategy
conquer-1.3.3 Convolution-Type Smoothed Quantile Regression
contfrac-1.1-12 Continued Fractions
conumee-1.40.0 Enhanced copy-number variation analysis using Illumina DNA methylation arrays
copCAR-2.0-4 Fitting the copCAR Regression Model for Discrete Areal Data
copula-1.1-4 Multivariate Dependence with Copulas
corpcor-1.6.10 Efficient Estimation of Covariance and (Partial) Correlation
corrplot-0.95 Visualization of a Correlation Matrix
covr-3.6.4 Test Coverage for Packages
covsim-1.1.0 VITA, IG and PLSIM Simulation for Given Covariance and Marginals
cowplot-1.1.3 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
coxed-0.3.3 Duration-Based Quantities of Interest for the Cox Proportional Hazards Model
coxme-2.2-22 Mixed Effects Cox Models
cpp11-0.5.0 A C++11 Interface for R’s C Interface
crayon-1.5.3 Colored Terminal Output
credentials-2.0.2 Tools for Managing SSH and Git Credentials
crfsuite-0.4.2 Conditional Random Fields for Labelling Sequential Data in Natural Language Processing
crosstalk-1.2.1 Inter-Widget Interactivity for HTML Widgets
crul-1.5.0 HTTP Client
csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
ctmle-0.1.2 Collaborative Targeted Maximum Likelihood Estimation
cubature-2.1.1 Adaptive Multivariate Integration over Hypercubes
cubelyr-1.0.2 A Data Cube ‘dplyr’ Backend
cummeRbund-2.48.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
curl-6.0.1 A Modern and Flexible Web Client for R
cvAUC-1.1.4 Cross-Validated Area Under the ROC Curve Confidence Intervals
cytolib-2.18.0 C++ infrastructure for representing and interacting with the gated cytometry data
d3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from R
dHSIC-2.1 Independence Testing via Hilbert Schmidt Independence Criterion
dada2-1.34.0 Accurate, high-resolution sample inference from amplicon sequencing data
dagitty-0.3-4 Graphical Analysis of Structural Causal Models
data.table-1.16.2 Extension of data.frame
data.tree-1.1.0 General Purpose Hierarchical Data Structure
datasets built in
datawizard-0.13.0 Easy Data Wrangling and Statistical Transformations
date-1.2-42 Functions for Handling Dates
dbarts-0.9-28 Discrete Bayesian Additive Regression Trees Sampler
dbplyr-2.5.0 A ‘dplyr’ Back End for Databases
dbscan-1.2-0 Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms
dcurver-0.9.2 Utility Functions for Davidian Curves
ddPCRclust-1.26.0 Clustering algorithm for ddPCR data
ddalpha-1.3.16 Depth-Based Classification and Calculation of Data Depth
deSolve-1.40 Solvers for Initial Value Problems of Differential Equations (‘ODE’, ‘DAE’, ‘DDE’)
deal-1.2-42 Learning Bayesian Networks with Mixed Variables
debugme-1.2.0 Debug R Packages
decontam-1.26.0 Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
decoupleR-2.12.0 decoupleR: Ensemble of computational methods to infer biological activities from omics data
deldir-2.0-4 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
dendextend-1.19.0 Extending ‘dendrogram’ Functionality in R
densEstBayes-1.0-2.2 Density Estimation via Bayesian Inference Engines
derfinder-1.40.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
derfinderHelper-1.40.0 derfinder helper package
desc-1.4.3 Manipulate DESCRIPTION Files
devtools-2.4.5 Tools to Make Developing R Packages Easier
dfidx-0.1-0 Indexed Data Frames
diagram-1.6.5 Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
dichromat-2.0-0.1 Color Schemes for Dichromats
diffcyt-1.26.0 Differential discovery in high-dimensional cytometry via high-resolution clustering
diffobj-0.3.5 Diffs for R Objects
digest-0.6.37 Create Compact Hash Digests of R Objects
dimRed-0.2.6 A Framework for Dimensionality Reduction
diptest-0.77-1 Hartigan’s Dip Test Statistic for Unimodality - Corrected
dir.expiry-1.14.0 Managing Expiration for Cache Directories
directlabels-2024.1.21 Direct Labels for Multicolor Plots
dismo-1.3-14 Species Distribution Modeling
distillery-1.2-1 Method Functions for Confidence Intervals and to Distill Information from an Object
distr-2.9.5 Object Oriented Implementation of Distributions
distrEx-2.9.5 Extensions of Package ‘distr’
distributional-0.5.0 Vectorised Probability Distributions
diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis Package
dlm-1.1-6.1 Bayesian and Likelihood Analysis of Dynamic Linear Models
doBy-4.6.24 Groupwise Statistics, LSmeans, Linear Estimates, Utilities
doMC-1.3.8 Foreach Parallel Adaptor for ‘parallel’
doParallel-1.0.17 Foreach Parallel Adaptor for the ‘parallel’ Package
doRNG-1.8.6 Generic Reproducible Parallel Backend for ‘foreach’ Loops
doSNOW-1.0.20 Foreach Parallel Adaptor for the ‘snow’ Package
doc2vec-0.2.0 Distributed Representations of Sentences, Documents and Topics
docopt-0.7.1 Command-Line Interface Specification Language
docstring-1.0.0 Provides Docstring Capabilities to R Functions
dotCall64-1.2 Enhanced Foreign Function Interface Supporting Long Vectors
downlit-0.4.4 Syntax Highlighting and Automatic Linking
downloader-0.4 Download Files over HTTP and HTTPS
dplyr-1.1.4 A Grammar of Data Manipulation
dqrng-0.4.1 Fast Pseudo Random Number Generators
dr-3.0.10 Methods for Dimension Reduction for Regression
dreamerr-1.4.0 Error Handling Made Easy
drgee-1.1.10 Doubly Robust Generalized Estimating Equations
drugCombo-1.2.1 Drug Interaction Modeling Based on Loewe Additivity Following Harbron’s Approach
dtangle-2.0.9 Cell Type Deconvolution from Gene Expressions
dtplyr-1.3.1 Data Table Back-End for ‘dplyr’
dtw-1.23-1 Dynamic Time Warping Algorithms
dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
dupRadar-1.36.0 Assessment of duplication rates in RNA-Seq datasets
dygraphs-1.1.1.6 Interface to ‘Dygraphs’ Interactive Time Series Charting Library
dynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering Dendrograms
e1071-1.7-16 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
earth-5.3.4 Multivariate Adaptive Regression Splines
edgeR-4.4.0 Empirical Analysis of Digital Gene Expression Data in R
egg-0.4.5 Extensions for ‘ggplot2’: Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size
ellipse-0.5.0 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
ellipsis-0.3.2 Tools for Working with …
elliptic-1.4-0 Weierstrass and Jacobi Elliptic Functions
emdbook-1.3.13 Support Functions and Data for “Ecological Models and Data”
emmeans-1.10.5 Estimated Marginal Means, aka Least-Squares Means
emoa-0.5-3 Evolutionary Multiobjective Optimization Algorithms
emulator-1.2-24 Bayesian Emulation of Computer Programs
energy-1.7-12 E-Statistics: Multivariate Inference via the Energy of Data
enrichplot-1.26.2 Visualization of Functional Enrichment Result
ensembldb-2.30.0 Utilities to create and use Ensembl-based annotation databases
entropy-1.3.1 Estimation of Entropy, Mutual Information and Related Quantities
epitools-0.5-10.1 Epidemiology Tools
ergm-4.7.5 Fit, Simulate and Diagnose Exponential-Family Models for Networks
ergm.count-4.1.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
ergm.multi-0.2.1.1 Fit, Simulate and Diagnose Exponential-Family Models for Multiple or Multilayer Networks
escape-2.2.1 Easy single cell analysis platform for enrichment
estimability-1.5.1 Tools for Assessing Estimability of Linear Predictions
evaluate-1.0.1 Parsing and Evaluation Tools that Provide More Details than the Default
evd-2.3-7.1 Functions for Extreme Value Distributions
expm-1.0-0 Matrix Exponential, Log, ‘etc’
expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
extRemes-2.1-4 Extreme Value Analysis
extraDistr-1.10.0 Additional Univariate and Multivariate Distributions
extrafont-0.19 Tools for Using Fonts
extrafontdb-1.0 Package for holding the database for the extrafont package
fANCOVA-0.6-1 Nonparametric Analysis of Covariance
factoextra-1.0.7 Extract and Visualize the Results of Multivariate Data Analyses
fail-1.3 File Abstraction Interface Layer (FAIL)
fansi-1.0.6 ANSI Control Sequence Aware String Functions
farver-2.1.2 High Performance Colour Space Manipulation
fastDummies-1.7.4 Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables
fastICA-1.2-5.1 FastICA Algorithms to Perform ICA and Projection Pursuit
fastcluster-1.2.6 Fast Hierarchical Clustering Routines for R and ‘Python’
fasterize-1.1.0 Fast Polygon to Raster Conversion
fastlogranktest-0.2.1 A Fast Way to Calculate the p-Value of One or Multiple Log-Rank-Tests
fastmap-1.2.0 Fast Data Structures
fastmatch-1.1-4 Fast ‘match()’ Function
fda-6.2.0 Functional Data Analysis
fdrtool-1.2.18 Estimation of (Local) False Discovery Rates and Higher Criticism
fds-1.8 Functional Data Sets
feather-0.3.5 R Bindings to the Feather ‘API’
feature-1.2.15 Local Inferential Feature Significance for Multivariate Kernel Density Estimation
ff-4.5.0 Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
fftw-1.0-9 Fast FFT and DCT Based on the FFTW Library
fftwtools-0.9-11 Wrapper for ‘FFTW3’ Includes: One-Dimensional, Two-Dimensional, Three-Dimensional, and Multivariate Transforms
fgsea-1.32.0 Fast Gene Set Enrichment Analysis
fields-16.3 Tools for Spatial Data
filehash-2.4-6 Simple Key-Value Database
filelock-1.0.3 Portable File Locking
finalfit-1.0.8 Quickly Create Elegant Regression Results Tables and Plots when Modelling
findpython-1.0.9 Functions to Find an Acceptable Python Binary
fishMod-0.29.2 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta Log-Normal Models
fitdistrplus-1.2-1 Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
fixest-0.12.1 Fast Fixed-Effects Estimations
flashClust-1.01-2 Implementation of optimal hierarchical clustering
flexclust-1.4-2 Flexible Cluster Algorithms
flexmix-2.3-19 Flexible Mixture Modeling
flextable-0.9.7 Functions for Tabular Reporting
flowAI-1.36.0 Automatic and interactive quality control for flow cytometry data
flowClean-1.44.0 flowClean
flowClust-3.44.0 Clustering for Flow Cytometry
flowCore-2.18.0 flowCore: Basic structures for flow cytometry data
flowDensity-1.40.0 Sequential Flow Cytometry Data Gating
flowFP-1.64.0 Fingerprinting for Flow Cytometry
flowMerge-2.54.0 Cluster Merging for Flow Cytometry Data
flowPeaks-1.52.0 An R package for flow data clustering
flowStats-4.18.0 Statistical methods for the analysis of flow cytometry data
flowViz-1.70.0 Visualization for flow cytometry
flowWorkspace-4.18.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
fma-2.5 Data Sets from “Forecasting: Methods and Applications” by Makridakis, Wheelwright & Hyndman (1998)
fmri-1.9.12.1 Analysis of fMRI Experiments
fontBitstreamVera-0.1.1 Fonts with ‘Bitstream Vera Fonts’ License
fontLiberation-0.1.0 Liberation Fonts
fontawesome-0.5.3 Easily Work with ‘Font Awesome’ Icons
fontquiver-0.2.1 Set of Installed Fonts
forcats-1.0.0 Tools for Working with Categorical Variables (Factors)
foreach-1.5.2 Provides Foreach Looping Construct
forecast-8.23.0 Forecasting Functions for Time Series and Linear Models
foreign-0.8-87 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …
formatR-1.14 Format R Code Automatically
formula.tools-1.7.1 Programmatic Utilities for Manipulating Formulas, Expressions, Calls, Assignments and Other R Objects
fossil-0.4.0 Palaeoecological and Palaeogeographical Analysis Tools
fpc-2.2-13 Flexible Procedures for Clustering
fpp-0.5 Data for “Forecasting: principles and practice”
fracdiff-1.5-3 Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
frbs-3.2-0 Fuzzy Rule-Based Systems for Classification and Regression Tasks
fresh-0.2.1 Create Custom ‘Bootstrap’ Themes to Use in ‘Shiny’
fs-1.6.5 Cross-Platform File System Operations Based on ‘libuv’
furrr-0.3.1 Apply Mapping Functions in Parallel using Futures
futile.logger-1.4.3 A Logging Utility for R
futile.options-1.0.1 Futile Options Management
future-1.34.0 Unified Parallel and Distributed Processing in R for Everyone
future.apply-1.11.3 Apply Function to Elements in Parallel using Futures
gWidgets2-1.0-9 Rewrite of gWidgets API for Simplified GUI Construction
gWidgets2tcltk-1.0-8 Toolkit Implementation of gWidgets2 for tcltk
gam-1.22-5 Generalized Additive Models
gamlss-5.4-22 Generalized Additive Models for Location Scale and Shape
gamlss.data-6.0-6 Data for Generalised Additive Models for Location Scale and Shape
gamlss.dist-6.1-1 Distributions for Generalized Additive Models for Location Scale and Shape
gamlss.tr-5.1-9 Generating and Fitting Truncated `gamlss.family’ Distributions
gamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
gap-1.6 Genetic Analysis Package
gap.datasets-0.0.6 Datasets for ‘gap’
gapfill-0.9.6-1 Fill Missing Values in Satellite Data
gargle-1.5.2 Utilities for Working with Google APIs
gaussquad-1.0-3 Collection of Functions for Gaussian Quadrature
gbRd-0.4.12 Utilities for Processing Rd Objects and Files
gbm-2.2.2 Generalized Boosted Regression Models
gclus-1.3.2 Clustering Graphics
gcmr-1.0.3 Gaussian Copula Marginal Regression
gcrma-2.78.0 Background Adjustment Using Sequence Information
gdalUtils-2.0.3.2 Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities
gdata-3.0.1 Various R Programming Tools for Data Manipulation
gdistance-1.6.4 Distances and Routes on Geographical Grids
gdsfmt-1.42.0 R Interface to CoreArray Genomic Data Structure (GDS) Files
gdtools-0.4.1 Utilities for Graphical Rendering and Fonts Management
gee-4.13-27 Generalized Estimation Equation Solver
geeM-0.10.1 Solve Generalized Estimating Equations
geepack-1.3.12 Generalized Estimating Equation Package
geex-1.1.1 An API for M-Estimation
geiger-2.0.11 Analysis of Evolutionary Diversification
geneLenDataBase 1.42.0 Package Not Found
genefilter-1.88.0 genefilter: methods for filtering genes from high-throughput experiments
geneplotter-1.84.0 Graphics related functions for Bioconductor
generics-0.1.3 Common S3 Generics not Provided by Base R Methods Related to Model Fitting
genoPlotR-0.8.11 Plot Publication-Grade Gene and Genome Maps
genomation-1.38.0 Summary, annotation and visualization of genomic data
geojsonsf-2.0.3 GeoJSON to Simple Feature Converter
geometries-0.2.4 Convert Between R Objects and Geometric Structures
geometry-0.5.0 Mesh Generation and Surface Tessellation
gert-2.1.4 Simple Git Client for R
getopt-1.20.4 C-Like ‘getopt’ Behavior
gfonts-0.2.0 Offline ‘Google’ Fonts for ‘Markdown’ and ‘Shiny’
ggExtra-0.10.1 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’ Enhancements
ggbeeswarm-0.7.2 Categorical Scatter (Violin Point) Plots
ggbio-1.54.0 Visualization tools for genomic data
ggcyto-1.34.0 Visualize Cytometry data with ggplot
ggdag-0.2.13 Analyze and Create Elegant Directed Acyclic Graphs
ggdendro-0.2.0 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
ggdist-3.3.2 Visualizations of Distributions and Uncertainty
ggfan-0.1.3 Summarise a Distribution Through Coloured Intervals
ggforce-0.4.2 Accelerating ‘ggplot2’
ggformula-0.12.0 Formula Interface to the Grammar of Graphics
ggfun-0.1.7 Miscellaneous Functions for ‘ggplot2’
ggh4x-0.2.8 Hacks for ‘ggplot2’
ggnetwork-0.5.13 Geometries to Plot Networks with ‘ggplot2’
ggnewscale-0.5.0 Multiple Fill and Colour Scales in ‘ggplot2’
ggplot2-3.5.1 Create Elegant Data Visualisations Using the Grammar of Graphics
ggplotify-0.1.2 Convert Plot to ‘grob’ or ‘ggplot’ Object
ggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plot
ggpubr-0.6.0 ‘ggplot2’ Based Publication Ready Plots
ggraph-2.2.1 An Implementation of Grammar of Graphics for Graphs and Networks
ggrastr-1.0.2 Rasterize Layers for ‘ggplot2’
ggrepel-0.9.6 Automatically Position Non-Overlapping Text Labels with ‘ggplot2’
ggridges-0.5.6 Ridgeline Plots in ‘ggplot2’
ggsci-3.2.0 Scientific Journal and Sci-Fi Themed Color Palettes for ‘ggplot2’
ggseqlogo-0.2 A ‘ggplot2’ Extension for Drawing Publication-Ready Sequence Logos
ggsignif-0.6.4 Significance Brackets for ‘ggplot2’
ggstance-0.3.7 Horizontal ‘ggplot2’ Components
ggstats-0.7.0 Extension to ‘ggplot2’ for Plotting Stats
ggtangle-0.0.4 Draw Network with Data
ggthemes-5.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’
ggtree-3.14.0 an R package for visualization of tree and annotation data
ggvenn-0.1.10 Draw Venn Diagram by ‘ggplot2’
ggvis-0.4.9 Interactive Grammar of Graphics
gh-1.4.1 ‘GitHub’ ‘API’
git2r-0.35.0 Provides Access to Git Repositories
gitcreds-0.1.2 Query ‘git’ Credentials from ‘R’
glasso-1.11 Graphical Lasso: Estimation of Gaussian Graphical Models
gld-2.6.6 Estimation and Use of the Generalised (Tukey) Lambda Distribution
gllvm-1.4.3 Generalized Linear Latent Variable Models
glmmML-1.1.7 Generalized Linear Models with Clustering
glmmTMB-1.1.10 Generalized Linear Mixed Models using Template Model Builder
glmnet-4.1-8 Lasso and Elastic-Net Regularized Generalized Linear Models
globals-0.16.3 Identify Global Objects in R Expressions
globaltest-5.60.0 Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
glue-1.8.0 Interpreted String Literals
gmm-1.8 Generalized Method of Moments and Generalized Empirical Likelihood
gmodels-2.19.1 Various R Programming Tools for Model Fitting
gmp-0.7-5 Multiple Precision Arithmetic
gnumeric-0.7-10 Read Data from Files Readable by ‘gnumeric’
goftest-1.2-3 Classical Goodness-of-Fit Tests for Univariate Distributions
goldilocks-0.3.0 Goldilocks Adaptive Trial Designs for Time-to-Event Endpoints
gomms-1.0 GLM-Based Ordination Method
googledrive-2.1.1 An Interface to Google Drive
googlesheets4-1.1.1 Access Google Sheets using the Sheets API V4
goseq-1.58.0 Gene Ontology analyser for RNA-seq and other length biased data
gower-1.0.1 Gower’s Distance
gplots-3.2.0 Various R Programming Tools for Plotting Data
grDevices built in
grImport2-0.3-3 Importing ‘SVG’ Graphics
graph-1.84.0 graph: A package to handle graph data structures
graphics built in
graphite-1.52.0 GRAPH Interaction from pathway Topological Environment
graphlayouts-1.2.1 Additional Layout Algorithms for Network Visualizations
grf-2.4.0 Generalized Random Forests
grid built in
gridBase-0.4-7 Integration of base and grid graphics
gridExtra-2.3 Miscellaneous Functions for “Grid” Graphics
gridGraphics-0.5-1 Redraw Base Graphics Using ‘grid’ Graphics
grpreg-3.5.0 Regularization Paths for Regression Models with Grouped Covariates
gsDesign-3.6.5 Group Sequential Design
gsalib-2.2.1 Utility Functions for ‘GATK’
gsignal-0.3-7 Signal Processing
gsl-2.1-8 Wrapper for the Gnu Scientific Library
gsmoothr-0.1.7 Smoothing tools
gson-0.1.0 Base Class and Methods for ‘gson’ Format
gsw-1.2-0 Gibbs Sea Water Functions
gt-0.11.1 Easily Create Presentation-Ready Display Tables
gtable-0.3.6 Arrange ‘Grobs’ in Tables
gtools-3.9.5 Various R Programming Tools
gtsummary-2.0.3 Presentation-Ready Data Summary and Analytic Result Tables
h2o-3.44.0.3 R Interface for the ‘H2O’ Scalable Machine Learning Platform
hahmmr-1.0.0 Haplotype-Aware Hidden Markov Model for RNA
hal9001-0.4.6 The Scalable Highly Adaptive Lasso
haldensify-0.2.3 Highly Adaptive Lasso Conditional Density Estimation
hardhat-1.4.0 Construct Modeling Packages
harmony-1.2.1 Fast, Sensitive, and Accurate Integration of Single Cell Data
hash-2.2.6.3 Full Featured Implementation of Hash Tables/Associative Arrays/Dictionaries
haven-2.5.4 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
hdf5r-1.3.11 Interface to the ‘HDF5’ Binary Data Format
hdm-0.3.2 High-Dimensional Metrics
hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
heatmap3-1.1.9 An Improved Heatmap Package
heatmaply-1.5.0 Interactive Cluster Heat Maps Using ‘plotly’ and ‘ggplot2’
here-1.0.1 A Simpler Way to Find Your Files
hexbin-1.28.5 Hexagonal Binning Routines
hgu133plus2.db 3.13.0 Package Not Found
highr-0.11 Syntax Highlighting for R Source Code
hms-1.1.3 Pretty Time of Day
htmlTable-2.4.3 Advanced Tables for Markdown/HTML
htmltools-0.5.8.1 Tools for HTML
htmlwidgets-1.6.4 HTML Widgets for R
httpcode-0.3.0 ‘HTTP’ Status Code Helper
httpuv-1.6.15 HTTP and WebSocket Server Library
httr-1.4.7 Tools for Working with URLs and HTTP
httr2-1.0.6 Perform HTTP Requests and Process the Responses
huge-1.3.5 High-Dimensional Undirected Graph Estimation
hunspell-3.0.5 High-Performance Stemmer, Tokenizer, and Spell Checker
hwriter-1.3.2.1 HTML Writer - Outputs R Objects in HTML Format
hypergeo-1.2-13 The Gauss Hypergeometric Function
ica-1.0-3 Independent Component Analysis
idr-1.3 Irreproducible Discovery Rate
ids-1.0.1 Generate Random Identifiers
ie2misc-0.9.1 Irucka Embry’s Miscellaneous USGS Functions
igraph-2.1.1 Network Analysis and Visualization
illuminaio-0.48.0 Parsing Illumina Microarray Output Files
image.binarization-0.1.3 Binarize Images for Enhancing Optical Character Recognition
imager-1.0.2 Image Processing Library Based on ‘CImg’
imagerExtra-1.3.2 Extra Image Processing Library Based on ‘imager’
impute-1.80.0 impute: Imputation for microarray data
ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
influenceR-0.1.5 Software Tools to Quantify Structural Importance of Nodes in a Network
infotheo-1.2.0.1 Information-Theoretic Measures
ini-0.3.1 Read and Write ‘.ini’ Files
inline-0.3.20 Functions to Inline C, C++, Fortran Function Calls from R
insight-0.20.5 Easy Access to Model Information for Various Model Objects
interactiveDisplayBase-1.44.0 Base package for enabling powerful shiny web displays of Bioconductor objects
intergraph-2.0-4 Coercion Routines for Network Data Objects
interp-1.1-6 Interpolation Methods
interpretR-0.2.5 Binary Classifier and Regression Model Interpretation Functions
intervals-0.15.5 Tools for Working with Points and Intervals
intrinsicDimension-1.2.0 Intrinsic Dimension Estimation
inum-1.0-5 Interval and Enum-Type Representation of Vectors
ipred-0.9-15 Improved Predictors
irace-3.5 Iterated Racing for Automatic Algorithm Configuration
irlba-2.3.5.1 Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices
ismev-1.42 An Introduction to Statistical Modeling of Extreme Values
isoband-0.2.7 Generate Isolines and Isobands from Regularly Spaced Elevation Grids
isva-1.9 Independent Surrogate Variable Analysis
iterators-1.0.14 Provides Iterator Construct
itertools-0.1-3 Iterator Tools
janeaustenr-1.0.0 Jane Austen’s Complete Novels
jiebaR-0.11 Chinese Text Segmentation
jiebaRD-0.1 Chinese Text Segmentation Data for jiebaR Package
jomo-2.7-6 Multilevel Joint Modelling Multiple Imputation
jpeg-0.1-10 Read and write JPEG images
jquerylib-0.1.4 Obtain ‘jQuery’ as an HTML Dependency Object
jsonify-1.2.2 Convert Between ‘R’ Objects and Javascript Object Notation (JSON)
jsonlite-1.8.9 A Simple and Robust JSON Parser and Generator for R
jstable-1.3.6 Create Tables from Different Types of Regression
juicyjuice-0.1.0 Inline CSS Properties into HTML Tags Using ‘juice’
kableExtra-1.4.0 Construct Complex Table with ‘kable’ and Pipe Syntax
kde1d-1.0.7 Univariate Kernel Density Estimation
kedd-1.0.4 Kernel Estimator and Bandwidth Selection for Density and Its Derivatives
kernlab-0.9-33 Kernel-Based Machine Learning Lab
kinship2-1.9.6.1 Pedigree Functions
klaR-1.7-3 Classification and Visualization
knitr-1.49 A General-Purpose Package for Dynamic Report Generation in R
kohonen-3.0.12 Supervised and Unsupervised Self-Organising Maps
ks-1.14.3 Kernel Smoothing
labdsv-2.1-0 Ordination and Multivariate Analysis for Ecology
labeling-0.4.3 Axis Labeling
labelled-2.13.0 Manipulating Labelled Data
laeken-0.5.3 Estimation of Indicators on Social Exclusion and Poverty
lambda.r-1.2.4 Modeling Data with Functional Programming
lars-1.3 Least Angle Regression, Lasso and Forward Stagewise
lassosum 0.4.5 Package Not Found
later-1.3.2 Utilities for Scheduling Functions to Execute Later with Event Loops
lattice-0.22-6 Trellis Graphics for R
latticeExtra-0.6-30 Extra Graphical Utilities Based on Lattice
lava-1.8.0 Latent Variable Models
lavaan-0.6-19 Latent Variable Analysis
lazy-1.2-18 Lazy Learning for Local Regression
lazyeval-0.2.2 Lazy (Non-Standard) Evaluation
lda-1.5.2 Collapsed Gibbs Sampling Methods for Topic Models
ldbounds-2.0.2 Lan-DeMets Method for Group Sequential Boundaries
leafem-0.2.3 ‘leaflet’ Extensions for ‘mapview’
leaflet-2.2.2 Create Interactive Web Maps with the JavaScript ‘Leaflet’ Library
leaflet.providers-2.0.0 Leaflet Providers
leafsync-0.1.0 Small Multiples for Leaflet Web Maps
leaps-3.2 Regression Subset Selection
leiden-0.4.3.1 R Implementation of Leiden Clustering Algorithm
lhs-1.2.0 Latin Hypercube Samples
libcoin-1.0-10 Linear Test Statistics for Permutation Inference
lifecycle-1.0.4 Manage the Life Cycle of your Package Functions
limSolve-1.5.7.1 Solving Linear Inverse Models
limma-3.62.1 Linear Models for Microarray and Omics Data
linkcomm-1.0-14 Tools for Generating, Visualizing, and Analysing Link Communities in Networks
linprog-0.9-4 Linear Programming / Optimization
liquidSVM-1.2.4 A Fast and Versatile SVM Package
listenv-0.9.1 Environments Behaving (Almost) as Lists
lme4-1.1-35.5 Linear Mixed-Effects Models using ‘Eigen’ and S4
lmerTest-3.1-3 Tests in Linear Mixed Effects Models
lmom-3.2 L-Moments
lmtest-0.9-40 Testing Linear Regression Models
lobstr-1.1.2 Visualize R Data Structures with Trees
locfdr-1.1-8 Computes Local False Discovery Rates
locfit-1.5-9.10 Local Regression, Likelihood and Density Estimation
log4r-0.4.4 A Fast and Lightweight Logging System for R, Based on ‘log4j’
logcondens-2.1.8 Estimate a Log-Concave Probability Density from Iid Observations
logger-0.4.0 A Lightweight, Modern and Flexible Logging Utility
logistf-1.26.0 Firth’s Bias-Reduced Logistic Regression
logspline-2.1.22 Routines for Logspline Density Estimation
longitudinal-1.1.13 Analysis of Multiple Time Course Data
longmemo-1.1-3 Statistics for Long-Memory Processes (Book Jan Beran), and Related Functionality
loo-2.8.0 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
lpSolve-5.6.22 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
lpSolveAPI-5.5.2.0-17.12 R Interface to ‘lp_solve’ Version 5.5.2.0
lpsymphony-1.34.0 Symphony integer linear programming solver in R
lqa-1.0-3 Penalized Likelihood Inference for GLMs
lsa-0.73.3 Latent Semantic Analysis
lsei-1.3-0 Solving Least Squares or Quadratic Programming Problems under Equality/Inequality Constraints
lslx-0.6.11 Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood or Least Squares
lubridate-1.9.3 Make Dealing with Dates a Little Easier
lumi-2.58.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
lwgeom-0.2-14 Bindings to Selected ‘liblwgeom’ Functions for Simple Features
mRMRe-2.1.2.2 Parallelized Minimum Redundancy, Maximum Relevance (mRMR)
maSigPro-1.78.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
magic-1.6-1 Create and Investigate Magic Squares
magick-2.8.5 Advanced Graphics and Image-Processing in R
magrittr-2.0.3 A Forward-Pipe Operator for R
manipulateWidget-0.11.1 Add Even More Interactivity to Interactive Charts
mapproj-1.2.11 Map Projections
maps-3.4.2.1 Draw Geographical Maps
maptools-1.1-8 Tools for Handling Spatial Objects
markdown-1.13 Render Markdown with ‘commonmark’
marray-1.84.0 Exploratory analysis for two-color spotted microarray data
mathjaxr-1.6-0 Using ‘Mathjax’ in Rd Files
matlab-1.0.4.1 ‘MATLAB’ Emulation Package
matrixStats-1.4.1 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
matrixcalc-1.0-6 Collection of Functions for Matrix Calculations
maxLik-1.5-2.1 Maximum Likelihood Estimation and Related Tools
maxlike-0.1-11 Model Species Distributions by Estimating the Probability of Occurrence Using Presence-Only Data
maxnet-0.1.4 Fitting ‘Maxent’ Species Distribution Models with ‘glmnet’
mboost-2.9-11 Model-Based Boosting
mclogit-0.9.6 Multinomial Logit Models, with or without Random Effects or Overdispersion
mclust-6.1.1 Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
mcmc-0.9-8 Markov Chain Monte Carlo
mcmcse-1.5-0 Monte Carlo Standard Errors for MCMC
mda-0.5-5 Mixture and Flexible Discriminant Analysis
medflex-0.6-10 Flexible Mediation Analysis Using Natural Effect Models
mediation-4.5.0 Causal Mediation Analysis
memisc-0.99.31.8.1 Management of Survey Data and Presentation of Analysis Results
memoise-2.0.1 ‘Memoisation’ of Functions
memuse-4.2-3 Memory Estimation Utilities
metaMA-3.1.3 Meta-Analysis for MicroArrays
metadat-1.2-0 Meta-Analysis Datasets
metafor-4.6-0 Meta-Analysis Package for R
metap-1.11 Meta-Analysis of Significance Values
metapod-1.14.0 Meta-Analyses on P-Values of Differential Analyses
methods built in
methylumi-2.52.0 Handle Illumina methylation data
mets-1.3.4 Analysis of Multivariate Event Times
mgcv-1.9-1 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
mgsub-1.7.3 Safe, Multiple, Simultaneous String Substitution
mhsmm-0.4.21 Inference for Hidden Markov and Semi-Markov Models
mi-1.1 Missing Data Imputation and Model Checking
mia-1.14.0 Microbiome analysis
mice-3.16.0 Multivariate Imputation by Chained Equations
miceadds-3.17-44 Some Additional Multiple Imputation Functions, Especially for ‘mice’
microbenchmark-1.5.0 Accurate Timing Functions
mime-0.12 Map Filenames to MIME Types
minerva-1.5.10 Maximal Information-Based Nonparametric Exploration for Variable Analysis
minfi-1.52.1 Analyze Illumina Infinium DNA methylation arrays
miniUI-0.1.1.1 Shiny UI Widgets for Small Screens
minpack.lm-1.2-4 R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds
minqa-1.2.8 Derivative-Free Optimization Algorithms by Quadratic Approximation
minty-0.0.4 Minimal Type Guesser
mirt-1.43 Multidimensional Item Response Theory
misc3d-0.9-1 Miscellaneous 3D Plots
miscTools-0.6-28 Miscellaneous Tools and Utilities
missForest-1.5 Nonparametric Missing Value Imputation using Random Forest
missMDA-1.19 Handling Missing Values with Multivariate Data Analysis
missMethyl-1.40.0 Analysing Illumina HumanMethylation BeadChip Data
mitml-0.4-5 Tools for Multiple Imputation in Multilevel Modeling
mitools-2.4 Tools for Multiple Imputation of Missing Data
mixOmics-6.30.0 Omics Data Integration Project
mixsqp-0.3-54 Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
mixtools-2.0.0 Tools for Analyzing Finite Mixture Models
mlbench-2.1-5 Machine Learning Benchmark Problems
mlegp-3.1.9 Maximum Likelihood Estimates of Gaussian Processes
mlogit-1.1-1 Multinomial Logit Models
mlr-2.19.2 Machine Learning in R
mlrMBO-1.1.5.1 Bayesian Optimization and Model-Based Optimization of Expensive Black-Box Functions
mltools-0.3.5 Machine Learning Tools
mnormt-2.1.1 The Multivariate Normal and t Distributions, and Their Truncated Versions
modelr-0.1.11 Modelling Functions that Work with the Pipe
modeltools-0.2-23 Tools and Classes for Statistical Models
momentfit-0.5 Methods of Moments
moments-0.14.1 Moments, Cumulants, Skewness, Kurtosis and Related Tests
mosaicCore-0.9.4.0 Common Utilities for Other MOSAIC-Family Packages
motifStack-1.50.0 Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
motifmatchr-1.28.0 Fast Motif Matching in R
mpath-0.4-2.26 Regularized Linear Models
msigdbr-7.5.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
msm-1.8.2 Multi-State Markov and Hidden Markov Models in Continuous Time
mstate-0.3.3 Data Preparation, Estimation and Prediction in Multi-State Models
multcomp-1.4-26 Simultaneous Inference in General Parametric Models
multcompView-0.1-10 Visualizations of Paired Comparisons
multicool-1.0.1 Permutations of Multisets in Cool-Lex Order
multipol-1.0-9 Multivariate Polynomials
multitaper-1.0-17 Spectral Analysis Tools using the Multitaper Method
multtest-2.62.0 Resampling-based multiple hypothesis testing
munsell-0.5.1 Utilities for Using Munsell Colours
muscat-1.20.0 Multi-sample multi-group scRNA-seq data analysis tools
mutoss-0.1-13 Unified Multiple Testing Procedures
mvabund-4.2.1 Statistical Methods for Analysing Multivariate Abundance Data
mvnfast-0.2.8 Fast Multivariate Normal and Student’s t Methods
mvtnorm-1.3-2 Multivariate Normal and t Distributions
mzID-1.44.0 An mzIdentML parser for R
mzR-2.40.0 parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
nabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low Dimensions
naniar-1.1.0 Data Structures, Summaries, and Visualisations for Missing Data
natserv-1.0.0 ‘NatureServe’ Interface
naturalsort-0.1.3 Natural Ordering
ncbit-2013.03.29.1 Retrieve and Build NBCI Taxonomic Data
ncdf4-1.23 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
ncdfFlow-2.52.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
network-1.18.2 Classes for Relational Data
networkDynamic-0.11.5 Dynamic Extensions for Network Objects
networkLite-1.0.5 An Simplified Implementation of the ‘network’ Package Functionality
neuRosim-0.2-14 Simulate fMRI Data
neuralnet-1.44.2 Training of Neural Networks
ngspatial-1.2-2 Fitting the Centered Autologistic and Sparse Spatial Generalized Linear Mixed Models for Areal Data
nleqslv-3.3.5 Solve Systems of Nonlinear Equations
nlme-3.1-166 Linear and Nonlinear Mixed Effects Models
nloptr-2.1.1 R Interface to NLopt
nlsem-0.8-1 Fitting Structural Equation Mixture Models
nnet-7.3-19 Feed-Forward Neural Networks and Multinomial Log-Linear Models
nnls-1.6 The Lawson-Hanson Algorithm for Non-Negative Least Squares (NNLS)
nonnest2-0.5-8 Tests of Non-Nested Models
nor1mix-1.3-3 Normal aka Gaussian 1-d Mixture Models
norm-1.0-11.1 Analysis of Multivariate Normal Datasets with Missing Values
nortest-1.0-4 Tests for Normality
np-0.60-17 Nonparametric Kernel Smoothing Methods for Mixed Data Types
npsurv-0.5-0 Nonparametric Survival Analysis
numDeriv-2016.8-1.1 Accurate Numerical Derivatives
numbat-1.4.2 Haplotype-Aware CNV Analysis from scRNA-Seq
oai-0.4.0 General Purpose ‘Oai-PMH’ Services Client
oce-1.8-3 Analysis of Oceanographic Data
oddsratio-2.0.1 Odds Ratio Calculation for GAM(M)s & GLM(M)s
officer-0.6.7 Manipulation of Microsoft Word and PowerPoint Documents
oligo-1.70.0 Preprocessing tools for oligonucleotide arrays
oligoClasses-1.68.0 Classes for high-throughput arrays supported by oligo and crlmm
ontologyIndex-2.12 Reading Ontologies into R
oompaBase-3.2.9 Class Unions, Matrix Operations, and Color Schemes for OOMPA
oompaData-3.1.4 Data to Illustrate OOMPA Algorithms
openCyto-2.18.0 Hierarchical Gating Pipeline for flow cytometry data
openair-2.18-2 Tools for the Analysis of Air Pollution Data
openssl-2.2.2 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
openxlsx-4.2.7.1 Read, Write and Edit xlsx Files
operator.tools-1.6.3 Utilities for Working with R’s Operators
optextras-2019-12.4 Tools to Support Optimization Possibly with Bounds and Masks
optimParallel-1.0-2 Parallel Version of the L-BFGS-B Optimization Method
optimr-2019-12.16 A Replacement and Extension of the ‘optim’ Function
optimx-2023-10.21 Expanded Replacement and Extension of the ‘optim’ Function
optmatch-0.10.8 Functions for Optimal Matching
optparse-1.7.5 Command Line Option Parser
ordinal-2023.12-4.1 Regression Models for Ordinal Data
org.Hs.eg.db 3.20.0 Package Not Found
org.Mm.eg.db 3.20.0 Package Not Found
org.Rn.eg.db 3.20.0 Package Not Found
origami-1.0.7 Generalized Framework for Cross-Validation
oro.nifti-0.11.4 Rigorous - ‘NIfTI’ + ‘ANALYZE’ + ‘AFNI’ : Input / Output
orthopolynom-1.0-6.1 Collection of Functions for Orthogonal and Orthonormal Polynomials
osqp-0.6.3.3 Quadratic Programming Solver using the ‘OSQP’ Library
outliers-0.15 Tests for Outliers
pROC-1.18.5 Display and Analyze ROC Curves
pRoloc-1.46.0 A unifying bioinformatics framework for spatial proteomics
pRolocGUI-2.16.0 Interactive visualisation of spatial proteomics data
pRolocdata 1.44.0 Package Not Found
packrat-0.9.2 A Dependency Management System for Projects and their R Package Dependencies
pacman-0.5.1 Package Management Tool
pammtools-0.5.93 Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis
pamr-1.57 Pam: Prediction Analysis for Microarrays
pan-1.9 Multiple Imputation for Multivariate Panel or Clustered Data
parallel built in
parallelDist-0.2.6 Parallel Distance Matrix Computation using Multiple Threads
parallelMap-1.5.1 Unified Interface to Parallelization Back-Ends
parallelly-1.39.0 Enhancing the ‘parallel’ Package
parsedate-1.3.1 Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats
party-1.3-17 A Laboratory for Recursive Partytioning
partykit-1.2-22 A Toolkit for Recursive Partytioning
pastecs-1.4.2 Package for Analysis of Space-Time Ecological Series
patchwork-1.3.0 The Composer of Plots
pathview-1.46.0 a tool set for pathway based data integration and visualization
pbapply-1.7-2 Adding Progress Bar to ‘*apply’ Functions
pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
pbkrtest-0.5.3 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models
pbmcapply-1.5.1 Tracking the Progress of Mc*pply with Progress Bar
pcaMethods-1.98.0 A collection of PCA methods
pcaPP-2.0-5 Robust PCA by Projection Pursuit
pdp-0.8.2 Partial Dependence Plots
pec-2023.04.12 Prediction Error Curves for Risk Prediction Models in Survival Analysis
penalized-0.9-52 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
penfa-0.1.1 Single- And Multiple-Group Penalized Factor Analysis
peperr-1.5 Parallelised Estimation of Prediction Error
performance-0.12.4 Assessment of Regression Models Performance
perm-1.0-0.4 Exact or Asymptotic Permutation Tests
permute-0.9-7 Functions for Generating Restricted Permutations of Data
phangorn-2.12.1 Phylogenetic Reconstruction and Analysis
pheatmap-1.0.12 Pretty Heatmaps
phylobase-0.8.12 Base Package for Phylogenetic Structures and Comparative Data
phyloseq-1.50.0 Handling and analysis of high-throughput microbiome census data
phytools-2.3-0 Phylogenetic Tools for Comparative Biology (and Other Things)
pillar-1.9.0 Coloured Formatting for Columns
pim-2.0.2 Fit Probabilistic Index Models
pinfsc50-1.3.0 Sequence (‘FASTA’), Annotation (‘GFF’) and Variants (‘VCF’) for 17 Samples of ‘P. Infestans” and 1 ‘P. Mirabilis’
pixmap-0.4-13 Bitmap Images / Pixel Maps
pkgbuild-1.4.5 Find Tools Needed to Build R Packages
pkgconfig-2.0.3 Private Configuration for ‘R’ Packages
pkgdown-2.1.1 Make Static HTML Documentation for a Package
pkgload-1.4.0 Simulate Package Installation and Attach
pkgmaker-0.32.10 Development Utilities for R Packages
plogr-0.2.0 The ‘plog’ C++ Logging Library
plot3D-1.4.1 Plotting Multi-Dimensional Data
plot3Drgl-1.0.4 Plotting Multi-Dimensional Data - Using ‘rgl’
plotly-4.10.4 Create Interactive Web Graphics via ‘plotly.js’
plotmo-3.6.4 Plot a Model’s Residuals, Response, and Partial Dependence Plots
plotrix-3.8-4 Various Plotting Functions
pls-2.8-5 Partial Least Squares and Principal Component Regression
plyr-1.8.9 Tools for Splitting, Applying and Combining Data
plyranges-1.26.0 A fluent interface for manipulating GenomicRanges
pmp-1.18.0 Peak Matrix Processing and signal batch correction for metabolomics datasets
png-0.1-8 Read and write PNG images
poLCA-1.6.0.1 Polytomous Variable Latent Class Analysis
polspline-1.1.25 Polynomial Spline Routines
polyclip-1.10-7 Polygon Clipping
polycor-0.8-1 Polychoric and Polyserial Correlations
polynom-1.4-1 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
posterior-1.6.0 Tools for Working with Posterior Distributions
poweRlaw-0.80.0 Analysis of Heavy Tailed Distributions
ppcor-1.1 Partial and Semi-Partial (Part) Correlation
prabclus-2.3-4 Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data
pracma-2.4.4 Practical Numerical Math Functions
praise-1.0.0 Praise Users
preprocessCore-1.68.0 A collection of pre-processing functions
preseqR-4.0.0 Predicting Species Accumulation Curves
prettyGraphs-2.1.6 Publication-Quality Graphics
prettyunits-1.2.0 Pretty, Human Readable Formatting of Quantities
princurve-2.1.6 Fit a Principal Curve in Arbitrary Dimension
processx-3.8.4 Execute and Control System Processes
prodlim-2024.06.25 Product-Limit Estimation for Censored Event History Analysis
profileModel-0.6.1 Profiling Inference Functions for Various Model Classes
proftools-0.99-3 Profile Output Processing Tools for R
profvis-0.4.0 Interactive Visualizations for Profiling R Code
progress-1.2.3 Terminal Progress Bars
progressr-0.15.1 An Inclusive, Unifying API for Progress Updates
projpred-2.8.0 Projection Predictive Feature Selection
promises-1.3.0 Abstractions for Promise-Based Asynchronous Programming
proto-1.0.0 Prototype Object-Based Programming
proxy-0.4-27 Distance and Similarity Measures
proxyC-0.4.1 Computes Proximity in Large Sparse Matrices
pryr-0.1.6 Tools for Computing on the Language
ps-1.8.1 List, Query, Manipulate System Processes
pscl-1.5.9 Political Science Computational Laboratory
pspline-1.0-20 Penalized Smoothing Splines
psych-2.4.6.26 Procedures for Psychological, Psychometric, and Personality Research
pulsar-0.3.11 Parallel Utilities for Lambda Selection along a Regularization Path
purrr-1.0.2 Functional Programming Tools
pvclust-2.2-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
pwalign-1.2.0 Perform pairwise sequence alignments
qap-0.1-2 Heuristics for the Quadratic Assignment Problem (QAP)
qgam-1.3.4 Smooth Additive Quantile Regression Models
qgraph-1.9.8 Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
qlcMatrix-0.9.8 Utility Sparse Matrix Functions for Quantitative Language Comparison
qqconf-1.3.2 Creates Simultaneous Testing Bands for QQ-Plots
qqman-0.1.9 Q-Q and Manhattan Plots for GWAS Data
qrng-0.0-10 (Randomized) Quasi-Random Number Generators
qrnn-2.1.1 Quantile Regression Neural Network
quadprog-1.5-8 Functions to Solve Quadratic Programming Problems
quanteda-4.1.0 Quantitative Analysis of Textual Data
quantmod-0.4.26 Quantitative Financial Modelling Framework
quantreg-5.99.1 Quantile Regression
quantsmooth-1.72.0 Quantile smoothing and genomic visualization of array data
questionr-0.7.8 Functions to Make Surveys Processing Easier
qvalue-2.38.0 Q-value estimation for false discovery rate control
r2rtf-1.1.1 Easily Create Production-Ready Rich Text Format (RTF) Tables and Figures
rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
rGADEM-2.54.0 de novo motif discovery
rJava-1.0-11 Low-Level R to Java Interface
ragg-1.3.3 Graphic Devices Based on AGG
rainbow-3.8 Bagplots, Boxplots and Rainbow Plots for Functional Data
random-0.2.6 True Random Numbers using RANDOM.ORG
randomForest-4.7-1.2 Breiman and Cutlers Random Forests for Classification and Regression
randomForestSRC-3.3.1 Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
randomcoloR-1.1.0.1 Generate Attractive Random Colors
randtoolbox-2.0.5 Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests
rangeModelMetadata-0.1.5 Provides Templates for Metadata Files Associated with Species Range Models
ranger-0.17.0 A Fast Implementation of Random Forests
rapidjsonr-1.2.0 ‘Rapidjson’ C++ Header Files
rappdirs-0.3.3 Application Directories: Determine Where to Save Data, Caches, and Logs
raster-3.6-30 Geographic Data Analysis and Modeling
rasterVis-0.51.6 Visualization Methods for Raster Data
ratelimitr-0.4.1 Rate Limiting for R
rbibutils-2.3 Read ‘Bibtex’ Files and Convert Between Bibliography Formats
rbiom-1.0.3 Read/Write, Analyze, and Visualize ‘BIOM’ Data
rbison-1.0.0 Interface to the ‘USGS’ ‘BISON’ API
rcmdcheck-1.4.0 Run ‘R CMD check’ from ‘R’ and Capture Results
rda-1.2-1 Shrunken Centroids Regularized Discriminant Analysis
rdrop2-0.8.2.1 Programmatic Interface to the ‘Dropbox’ API
reactR-0.6.1 React Helpers
reactable-0.4.4 Interactive Data Tables for R
reactome.db 1.89.0 Package Not Found
readODS-2.3.1 Read and Write ODS Files
readbitmap-0.1.5 Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF)
reader-1.0.6 Suite of Functions to Flexibly Read Data from Files
readr-2.1.5 Read Rectangular Text Data
readxl-1.4.3 Read Excel Files
rebird-1.3.0 R Client for the eBird Database of Bird Observations
recipes-1.1.0 Preprocessing and Feature Engineering Steps for Modeling
reformulas-0.4.0 Machinery for Processing Random Effect Formulas
regioneR-1.38.0 Association analysis of genomic regions based on permutation tests
registry-0.5-1 Infrastructure for R Package Registries
regsem-1.9.5 Regularized Structural Equation Modeling
reldist-1.7-2 Relative Distribution Methods
relsurv-2.2-9 Relative Survival
remaCor-0.0.18 Random Effects Meta-Analysis for Correlated Test Statistics
rematch-2.0.0 Match Regular Expressions with a Nicer ‘API’
rematch2-2.1.2 Tidy Output from Regular Expression Matching
remotes-2.5.0 R Package Installation from Remote Repositories, Including ‘GitHub’
rentrez-1.2.3 ‘Entrez’ in R
renv-1.0.11 Project Environments
reprex-2.1.1 Prepare Reproducible Example Code via the Clipboard
resample-0.6 Resampling Functions
reshape-0.8.9 Flexibly Reshape Data
reshape2-1.4.4 Flexibly Reshape Data: A Reboot of the Reshape Package
restfulr-0.0.15 R Interface to RESTful Web Services
reticulate-1.40.0 Interface to ‘Python’
rex-1.2.1 Friendly Regular Expressions
rgbif-3.8.1 Interface to the Global Biodiversity Information Facility API
rgdal-1.6-7 Bindings for the ‘Geospatial’ Data Abstraction Library
rgeos-0.6-4 Interface to Geometry Engine - Open Source (‘GEOS’)
rgexf-0.16.3 Build, Import, and Export GEXF Graph Files
rgl-1.3.14 3D Visualization Using OpenGL
rhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Library
rhdf5-2.50.0 R Interface to HDF5
rhdf5filters-1.18.0 HDF5 Compression Filters
ridge-3.3 Ridge Regression with Automatic Selection of the Penalty Parameter
ridigbio-0.4.1 Interface to the iDigBio Data API
rio-1.2.3 A Swiss-Army Knife for Data I/O
riskRegression-2023.12.21 Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks
ritis-1.0.0 Integrated Taxonomic Information System Client
rjson-0.2.23 JSON for R
rlang-1.1.4 Functions for Base Types and Core R and ‘Tidyverse’ Features
rle-0.9.2 Common Functions for Run-Length Encoded Vectors
rlecuyer-0.3-8 R Interface to RNG with Multiple Streams
rlemon-0.2.1 R Access to LEMON Graph Algorithms
rlist-0.4.6.2 A Toolbox for Non-Tabular Data Manipulation
rmarkdown-2.29 Dynamic Documents for R
rmeta-3.0 Meta-Analysis
rms-6.8-2 Regression Modeling Strategies
rncl-0.8.7 An Interface to the Nexus Class Library
rnetcarto-0.2.6 Fast Network Modularity and Roles Computation by Simulated Annealing (Rgraph C Library Wrapper for R)
rngWELL-0.10-10 Toolbox for WELL Random Number Generators
rngtools-1.5.2 Utility Functions for Working with Random Number Generators
robustbase-0.99-4-1 Basic Robust Statistics
rols-3.2.0 An R interface to the Ontology Lookup Service
rootSolve-1.8.2.4 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
ropls-1.38.0 PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
roptim-0.1.6 General Purpose Optimization in R using C++
rotl-3.1.0 Interface to the ‘Open Tree of Life’ API
roxygen2-7.3.2 In-Line Documentation for R
rpact-4.1.0 Confirmatory Adaptive Clinical Trial Design and Analysis
rpart-4.1.23 Recursive Partitioning and Regression Trees
rpf-1.0.14 Response Probability Functions
rprojroot-2.0.4 Finding Files in Project Subdirectories
rrcov-1.7-6 Scalable Robust Estimators with High Breakdown Point
rredlist-0.7.1 ‘IUCN’ Red List Client
rsample-1.2.1 General Resampling Infrastructure
rsconnect-1.3.3 Deploy Docs, Apps, and APIs to ‘Posit Connect’, ‘shinyapps.io’, and ‘RPubs’
rstan-2.32.6 R Interface to Stan
rstantools-2.4.0 Tools for Developing R Packages Interfacing with ‘Stan’
rstatix-0.7.2 Pipe-Friendly Framework for Basic Statistical Tests
rstudioapi-0.17.1 Safely Access the RStudio API
rsvd-1.0.5 Randomized Singular Value Decomposition
rtdists-0.11-5 Response Time Distributions
rtracklayer-1.66.0 R interface to genome annotation files and the UCSC genome browser
ruv-0.9.7.1 Detect and Remove Unwanted Variation using Negative Controls
rversions-2.1.2 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
rvertnet-0.8.4 Search ‘Vertnet’, a ‘Database’ of Vertebrate Specimen Records
rvest-1.0.4 Easily Harvest (Scrape) Web Pages
rvinecopulib-0.6.3.1.1 High Performance Algorithms for Vine Copula Modeling
s2-1.1.7 Spherical Geometry Operators Using the S2 Geometry Library
sampling-2.10 Survey Sampling
samr-3.0 SAM: Significance Analysis of Microarrays
sandwich-3.1-1 Robust Covariance Matrix Estimators
sass-0.4.9 Syntactically Awesome Style Sheets (‘Sass’)
scDblFinder-1.20.0 scDblFinder
scales-1.3.0 Scale Functions for Visualization
scam-1.2-17 Shape Constrained Additive Models
scater-1.34.0 Single-Cell Analysis Toolkit for Gene Expression Data in R
scattermore-1.2 Scatterplots with More Points
scatterpie-0.2.4 Scatter Pie Plot
scatterplot3d-0.3-44 3D Scatter Plot
scistreer-1.2.0 Maximum-Likelihood Perfect Phylogeny Inference at Scale
scran-1.34.0 Methods for Single-Cell RNA-Seq Data Analysis
scrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
scs-3.2.4 Splitting Conic Solver
sctransform-0.4.1 Variance Stabilizing Transformations for Single Cell UMI Data
scuttle-1.16.0 Single-Cell RNA-Seq Analysis Utilities
seewave-2.2.3 Sound Analysis and Synthesis
segmented-2.1-3 Regression Models with Break-Points / Change-Points Estimation (with Possibly Random Effects)
selectr-0.4-2 Translate CSS Selectors to XPath Expressions
sem-3.1-16 Structural Equation Models
semPLS-1.0-10 Structural Equation Modeling Using Partial Least Squares
semTools-0.5-6 Useful Tools for Structural Equation Modeling
sendmailR-1.4-0 Send Email Using R
sensemakr-0.1.6 Sensitivity Analysis Tools for Regression Models
sentometrics-1.0.0 An Integrated Framework for Textual Sentiment Time Series Aggregation and Prediction
seqLogo-1.72.0 Sequence logos for DNA sequence alignments
seqPattern-1.38.0 Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
seqinr-4.2-36 Biological Sequences Retrieval and Analysis
seriation-1.5.6 Infrastructure for Ordering Objects Using Seriation
servr-0.32 A Simple HTTP Server to Serve Static Files or Dynamic Documents
sessioninfo-1.2.2 R Session Information
setRNG-2024.2-1 Set (Normal) Random Number Generator and Seed
sf-1.0-19 Simple Features for R
sfheaders-0.4.4 Converts Between R Objects and Simple Feature Objects
sfsmisc-1.1-20 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
shadowtext-0.1.4 Shadow Text Grob and Layer
shape-1.4.6.1 Functions for Plotting Graphical Shapes, Colors
shapefiles-0.7.2 Read and Write ESRI Shapefiles
shiny-1.9.1 Web Application Framework for R
shinyBS-0.61.1 Twitter Bootstrap Components for Shiny
shinyFiles-0.9.3 A Server-Side File System Viewer for Shiny
shinyWidgets-0.8.7 Custom Inputs Widgets for Shiny
shinycssloaders-1.1.0 Add Loading Animations to a ‘shiny’ Output While It’s Recalculating
shinydashboard-0.7.2 Create Dashboards with ‘Shiny’
shinydashboardPlus-2.0.5 Add More ‘AdminLTE2’ Components to ‘shinydashboard’
shinyhelper-0.3.2 Easily Add Markdown Help Files to ‘shiny’ App Elements
shinyjs-2.1.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
shinypanel-0.1.5 Shiny Control Panel
shinystan-2.6.0 Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
shinythemes-1.2.0 Themes for Shiny
siggenes-1.80.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
signal-1.8-1 Signal Processing
simex-1.8 SIMEX- And MCSIMEX-Algorithm for Measurement Error Models
simona-1.4.0 Semantic Similarity on Bio-Ontologies
simplifyEnrichment-2.0.0 Simplify Functional Enrichment Results
sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header Files
slam-0.1-55 Sparse Lightweight Arrays and Matrices
slider-0.3.2 Sliding Window Functions
slingshot-2.14.0 Tools for ordering single-cell sequencing
sm-2.2-6.0 Smoothing Methods for Nonparametric Regression and Density Estimation
smoof-1.6.0.3 Single and Multi-Objective Optimization Test Functions
smoother-1.3 Functions Relating to the Smoothing of Numerical Data
sn-2.1.1 The Skew-Normal and Related Distributions Such as the Skew-t and the SUN
sna-2.8 Tools for Social Network Analysis
snow-0.4-4 Simple Network of Workstations
snowfall-1.84-6.3 Easier Cluster Computing (Based on ‘snow’)
snpStats-1.56.0 SnpMatrix and XSnpMatrix classes and methods
solrium-1.2.0 General Purpose R Interface to ‘Solr’
som-0.3-5.2 Self-Organizing Map
soundecology-1.3.3 Soundscape Ecology
sourcetools-0.1.7-1 Tools for Reading, Tokenizing and Parsing R Code
sp-2.1-4 Classes and Methods for Spatial Data
spData-2.3.3 Datasets for Spatial Analysis
spThin-0.2.0 Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models
spaMM-4.5.0 Mixed-Effect Models, with or without Spatial Random Effects
spaa-0.2.2 SPecies Association Analysis
spacefillr-0.3.3 Space-Filling Random and Quasi-Random Sequences
spam-2.11-0 SPArse Matrix
sparseMatrixStats-1.18.0 Summary Statistics for Rows and Columns of Sparse Matrices
sparsesvd-0.2-2 Sparse Truncated Singular Value Decomposition (from ‘SVDLIBC’)
spatial-7.3-17 Functions for Kriging and Point Pattern Analysis
spatstat-3.3-0 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
spatstat.core-2.4-4 Core Functionality of the ‘spatstat’ Family
spatstat.data-3.1-4 Datasets for ‘spatstat’ Family
spatstat.explore-3.3-3 Exploratory Data Analysis for the ‘spatstat’ Family
spatstat.geom-3.3-4 Geometrical Functionality of the ‘spatstat’ Family
spatstat.linnet-3.2-3 Linear Networks Functionality of the ‘spatstat’ Family
spatstat.model-3.3-3 Parametric Statistical Modelling and Inference for the ‘spatstat’ Family
spatstat.random-3.3-2 Random Generation Functionality for the ‘spatstat’ Family
spatstat.sparse-3.1-0 Sparse Three-Dimensional Arrays and Linear Algebra Utilities
spatstat.univar-3.1-1 One-Dimensional Probability Distribution Support for the ‘spatstat’ Family
spatstat.utils-3.1-1 Utility Functions for ‘spatstat’
spdep-1.3-6 Spatial Dependence: Weighting Schemes, Statistics
splancs-2.01-45 Spatial and Space-Time Point Pattern Analysis
splines built in
splitstackshape-1.4.8 Stack and Reshape Datasets After Splitting Concatenated Values
spls-2.2-3 Sparse Partial Least Squares (SPLS) Regression and Classification
spocc-1.2.3 Interface to Species Occurrence Data Sources
stabledist-0.7-2 Stable Distribution Functions
stabs-0.6-4 Stability Selection with Error Control
stageR-1.28.0 stageR: stage-wise analysis of high throughput gene expression data in R
stargazer-5.2.3 Well-Formatted Regression and Summary Statistics Tables
stars-0.6-7 Spatiotemporal Arrays, Raster and Vector Data Cubes
startupmsg-0.9.7 Utilities for Start-Up Messages
statmod-1.5.0 Statistical Modeling
statnet-2019.6 Software Tools for the Statistical Analysis of Network Data
statnet.common-4.10.0 Common R Scripts and Utilities Used by the Statnet Project Software
stats built in
stats4 built in
stdReg-3.4.1 Regression Standardization
stopwords-2.3 Multilingual Stopword Lists
stringdist-0.9.12 Approximate String Matching, Fuzzy Text Search, and String Distance Functions
stringi-1.8.4 Fast and Portable Character String Processing Facilities
stringmagic-1.1.2 Character String Operations and Interpolation, Magic Edition
stringr-1.5.1 Simple, Consistent Wrappers for Common String Operations
strucchange-1.5-4 Testing, Monitoring, and Dating Structural Changes
struct-1.18.0 Statistics in R Using Class-based Templates
structToolbox-1.18.0 Data processing & analysis tools for Metabolomics and other omics
styler-1.10.3 Non-Invasive Pretty Printing of R Code
subplex-1.9 Unconstrained Optimization using the Subplex Algorithm
survey-4.4-2 Analysis of Complex Survey Samples
survival-3.7-0 Survival Analysis
survivalROC-1.0.3.1 Time-Dependent ROC Curve Estimation from Censored Survival Data
susieR-0.12.35 Sum of Single Effects Linear Regression
svUnit-1.0.6 ‘SciViews’ - Unit, Integration and System Testing
sva-3.54.0 Surrogate Variable Analysis
svd-0.5.7 Interfaces to Various State-of-Art SVD and Eigensolvers
svglite-2.1.3 An ‘SVG’ Graphics Device
swagger-5.17.14.1 Dynamically Generates Documentation from a ‘Swagger’ Compliant API
symmoments-1.2.1 Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution
sys-3.4.3 Powerful and Reliable Tools for Running System Commands in R
systemfonts-1.1.0 System Native Font Finding
tableone-0.13.2 Create ‘Table 1’ to Describe Baseline Characteristics with or without Propensity Score Weights
tabletools 0.1.0 Package Not Found
tau-0.0-26 Text Analysis Utilities
taxize-0.9.100.1 Taxonomic Information from Around the Web
tcltk built in
tcltk2-1.2-11 Tcl/Tk Additions
tclust-2.0-5 Robust Trimmed Clustering
tensor-1.5 Tensor product of arrays
tensorA-0.36.2.1 Advanced Tensor Arithmetic with Named Indices
tergm-4.2.1 Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
terra-1.7-83 Spatial Data Analysis
testit-0.13 A Simple Package for Testing R Packages
testthat-3.2.1.1 Unit Testing for R
textcat-1.0-9 N-Gram Based Text Categorization
textplot-0.2.2 Text Plots
textshaping-0.4.0 Bindings to the ‘HarfBuzz’ and ‘Fribidi’ Libraries for Text Shaping
threejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globes
tibble-3.2.1 Simple Data Frames
tictoc-1.2.1 Functions for Timing R Scripts, as Well as Implementations of “Stack” and “StackList” Structures
tidybayes-3.0.7 Tidy Data and ‘Geoms’ for Bayesian Models
tidygraph-1.3.1 A Tidy API for Graph Manipulation
tidyr-1.3.1 Tidy Messy Data
tidyselect-1.2.1 Select from a Set of Strings
tidytext-0.4.2 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Tools
tidytree-0.4.6 A Tidy Tool for Phylogenetic Tree Data Manipulation
tidyverse-2.0.0 Easily Install and Load the ‘Tidyverse’
tiff-0.1-12 Read and Write TIFF Images
timeDate-4041.110 Rmetrics - Chronological and Calendar Objects
timechange-0.3.0 Efficient Manipulation of Date-Times
timereg-2.0.6 Flexible Regression Models for Survival Data
tinytex-0.54 Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
tkWidgets-1.84.0 R based tk widgets
tkrplot-0.0-27 TK Rplot
tm-0.7-15 Text Mining Package
tmap-3.3-4 Thematic Maps
tmaptools-3.1-1 Thematic Map Tools
tmle-2.0.1.1 Targeted Maximum Likelihood Estimation
tmvnsim-1.0-2 Truncated Multivariate Normal Simulation
tmvtnorm-1.6 Truncated Multivariate Normal and Student t Distribution
tokenizers-0.3.0 Fast, Consistent Tokenization of Natural Language Text
tools built in
topicmodels-0.2-17 Topic Models
tree-1.0-43 Classification and Regression Trees
treeio-1.30.0 Base Classes and Functions for Phylogenetic Tree Input and Output
triebeard-0.4.1 ‘Radix’ Trees in ‘Rcpp’
trimcluster-0.1-5 Cluster Analysis with Trimming
tripack-1.3-9.2 Triangulation of Irregularly Spaced Data
truncnorm-1.0-9 Truncated Normal Distribution
trust-0.1-8 Trust Region Optimization
tseries-0.10-58 Time Series Analysis and Computational Finance
tseriesChaos-0.1-13.1 Analysis of Nonlinear Time Series
tsna-0.3.5 Tools for Temporal Social Network Analysis
tsne-0.1-3.1 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
tuneR-1.4.7 Analysis of Music and Speech
twang-2.6.1 Toolkit for Weighting and Analysis of Nonequivalent Groups
tweedie-2.3.5 Evaluation of Tweedie Exponential Family Models
tweenr-2.0.3 Interpolate Data for Smooth Animations
txdbmaker-1.2.0 Tools for making TxDb objects from genomic annotations
tximport-1.34.0 Import and summarize transcript-level estimates for transcript- and gene-level analysis
tzdb-0.4.0 Time Zone Database Information
ucminf-1.2.2 General-Purpose Unconstrained Non-Linear Optimization
udpipe-0.8.11 Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the ‘UDPipe’ ‘NLP’ Toolkit
umap-0.2.10.0 Uniform Manifold Approximation and Projection
unbalanced-2.0 Racing for Unbalanced Methods Selection
unikn-1.0.0 Graphical Elements of the University of Konstanz’s Corporate Design
uniqueAtomMat-0.1-3-2 Finding Unique or Duplicated Rows or Columns for Atomic Matrices
units-0.8-5 Measurement Units for R Vectors
universalmotif-1.24.2 Import, Modify, and Export Motifs with R
unmarked-1.4.3 Models for Data from Unmarked Animals
urca-1.3-4 Unit Root and Cointegration Tests for Time Series Data
urlchecker-1.0.1 Run CRAN URL Checks from Older R Versions
urltools-1.7.3 Vectorised Tools for URL Handling and Parsing
uroot-2.1-3 Unit Root Tests for Seasonal Time Series
usethis-3.0.0 Automate Package and Project Setup
utf8-1.2.4 Unicode Text Processing
utils built in
uuid-1.2-1 Tools for Generating and Handling of UUIDs
uwot-0.2.2 The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
varhandle-2.0.6 Functions for Robust Variable Handling
variancePartition-1.36.2 Quantify and interpret drivers of variation in multilevel gene expression experiments
vcd-1.4-13 Visualizing Categorical Data
vcfR-1.15.0 Manipulate and Visualize VCF Data
vctrs-0.6.5 Vector Helpers
vegan-2.6-8 Community Ecology Package
venn-1.12 Draw Venn Diagrams
vioplot-0.5.0 Violin Plot
vipor-0.4.7 Plot Categorical Data Using Quasirandom Noise and Density Estimates
viridis-0.6.5 Colorblind-Friendly Color Maps for R
viridisLite-0.4.2 Colorblind-Friendly Color Maps (Lite Version)
visNetwork-2.1.2 Network Visualization using ‘vis.js’ Library
visdat-0.6.0 Preliminary Visualisation of Data
vroom-1.6.5 Read and Write Rectangular Text Data Quickly
vsn-3.74.0 Variance stabilization and calibration for microarray data
waiter-0.2.5 Loading Screen for ‘Shiny’
waldo-0.6.1 Find Differences Between R Objects
warp-0.2.1 Group Dates
wateRmelon-2.12.0 Illumina DNA methylation array normalization and metrics
waveslim-1.8.5 Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing
wdm-0.2.4 Weighted Dependence Measures
webshot-0.5.5 Take Screenshots of Web Pages
webutils-1.2.2 Utility Functions for Developing Web Applications
weights-1.0.4 Weighting and Weighted Statistics
wellknown-0.7.4 Convert Between ‘WKT’ and ‘GeoJSON’
whisker-0.4.1 for R, Logicless Templating
widgetTools-1.84.0 Creates an interactive tcltk widget
widgetframe-0.3.1 ‘Htmlwidgets’ in Responsive ‘iframes’
wikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’
withr-3.0.2 Run Code ‘With’ Temporarily Modified Global State
wk-0.9.4 Lightweight Well-Known Geometry Parsing
word2vec-0.4.0 Distributed Representations of Words
wordcloud-2.6 Word Clouds
worrms-0.4.3 World Register of Marine Species (WoRMS) Client
writexl-1.5.1 Export Data Frames to Excel ‘xlsx’ Format
xcms-4.4.0 LC-MS and GC-MS Data Analysis
xfun-0.49 Supporting Functions for Packages Maintained by ‘Yihui Xie’
xgboost-1.7.8.1 Extreme Gradient Boosting
xlsx-0.6.5 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
xlsxjars-0.6.1 Package required POI jars for the xlsx package
xml2-1.3.6 Parse XML
xopen-1.0.1 Open System Files, ‘URLs’, Anything
xtable-1.8-4 Export Tables to LaTeX or HTML
xts-0.14.1 eXtensible Time Series
yaImpute-1.0-34.1 Nearest Neighbor Observation Imputation and Evaluation Tools
yaml-2.3.10 Methods to Convert R Data to YAML and Back
yulab.utils-0.1.8 Supporting Functions for Packages Maintained by ‘YuLab-SMU’
zCompositions-1.5.0-4 Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
zeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignment
zellkonverter-1.16.0 Conversion Between scRNA-seq Objects
zip-2.3.1 Cross-Platform ‘zip’ Compression
zlibbioc-1.52.0 An R packaged zlib-1.2.5
zoo-1.8-12 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)

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