Known Issues
Package List
- ADGofTest-0.3 Anderson-Darling GoF test
- ALDEx2-1.36.0 Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
- ALL-1.46.0 A data package
- AgiMicroRna-2.54.0 Processing and Differential Expression Analysis of Agilent microRNA chips
- AnnotationDbi-1.66.0 Manipulation of SQLite-based annotations in Bioconductor
- AnnotationFilter-1.28.0 Facilities for Filtering Bioconductor Annotation Resources
- AnnotationForge-1.46.0 Tools for building SQLite-based annotation data packages
- AnnotationHub-3.12.0 Client to access AnnotationHub resources
- ArchR 1.0.2 [CRAN]
- BDgraph-2.72 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
- BH-1.84.0-0 Boost C++ Header Files
- BSgenome-1.72.0 Software infrastructure for efficient representation of full genomes and their SNPs
- BSgenome.Hsapiens.UCSC.hg19-1.4.3 Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)
- Bhat-0.9-12 General Likelihood Exploration
- BiasedUrn-2.0.11 Biased Urn Model Distributions
- Biobase-2.64.0 Biobase: Base functions for Bioconductor
- BiocBaseUtils-1.6.0 General utility functions for developing Bioconductor packages
- BiocFileCache-2.12.0 Manage Files Across Sessions
- BiocGenerics-0.50.0 S4 generic functions used in Bioconductor
- BiocIO-1.14.0 Standard Input and Output for Bioconductor Packages
- BiocManager-1.30.23 Access the Bioconductor Project Package Repository
- BiocNeighbors-1.22.0 Nearest Neighbor Detection for Bioconductor Packages
- BiocParallel-1.38.0 Bioconductor facilities for parallel evaluation
- BiocSingular-1.20.0 Singular Value Decomposition for Bioconductor Packages
- BiocStyle-2.32.0 Standard styles for vignettes and other Bioconductor documents
- BiocVersion-3.19.1 Set the appropriate version of Bioconductor packages
- Biostrings-2.72.0 Efficient manipulation of biological strings
- BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
- Bolstad-0.2-41 Functions for Elementary Bayesian Inference
- Bolstad2-1.0-29 Bolstad Functions
- BradleyTerry2-1.1-2 Bradley-Terry Models
- CATALYST-1.28.0 Cytometry dATa anALYSis Tools
- CGHbase-1.64.0 CGHbase: Base functions and classes for arrayCGH data analysis.
- CLONETv2-2.2.1 Clonality Estimates in Tumor
- CMA-1.62.0 Synthesis of microarray-based classification
- CNEr-1.40.0 CNE Detection and Visualization
- COMPASS-1.42.0 Combinatorial Polyfunctionality Analysis of Single Cells
- CVXR-1.0-12 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-2.70.0 Category Analysis
- ChIPQC-1.40.0 Quality metrics for ChIPseq data
- ChIPpeakAnno-3.38.0 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-1.40.0 ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
- ComplexHeatmap-2.20.0 Make Complex Heatmaps
- ConsensusClusterPlus-1.68.0 ConsensusClusterPlus
- CytoML-2.16.0 A GatingML Interface for Cross Platform Cytometry Data Sharing
- DAAG-1.25.4 Data Analysis and Graphics Data and Functions
- DECIPHER-3.0.0 Tools for curating, analyzing, and manipulating biological sequences
- DEGseq-1.58.0 Identify Differentially Expressed Genes from RNA-seq data
- DESeq2-1.44.0 Differential gene expression analysis based on the negative binomial distribution
- DEoptimR-1.1-3 Differential Evolution Optimization in Pure R
- DNAcopy-1.78.0 DNA Copy Number Data Analysis
- DO.db-2.9 A set of annotation maps describing the entire Disease Ontology
- DOSE-3.30.0 Disease Ontology Semantic and Enrichment analysis
- DOT-0.1 Render and Export DOT Graphs in R
- DT-0.33 A Wrapper of the JavaScript Library ‘DataTables’
- DelayedArray-0.30.1 A unified framework for working transparently with on-disk and in-memory array-like datasets
- DelayedMatrixStats-1.26.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
- Deriv-4.1.3 Symbolic Differentiation
- DiffBind-3.14.0 Differential Binding Analysis of ChIP-Seq Peak Data
- DirichletMultinomial-1.46.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
- DynDoc-1.82.0 Dynamic document tools
- EBImage-4.46.0 Image processing and analysis toolbox for R
- ECOSolveR-0.5.5 Embedded Conic Solver in R
- EpiModel-2.4.0 Mathematical Modeling of Infectious Disease Dynamics
- ExperimentHub-2.12.0 Client to access ExperimentHub resources
- FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
- FNN-1.1.4 Fast Nearest Neighbor Search Algorithms and Applications
- FlowSOM-2.12.0 Using self-organizing maps for visualization and interpretation of cytometry data
- Formula-1.2-5 Extended Model Formulas
- GEOquery-2.72.0 Get data from NCBI Gene Expression Omnibus (GEO)
- GGally-2.2.1 Extension to ‘ggplot2’
- GO.db-3.19.1 A set of annotation maps describing the entire Gene Ontology
- GOSemSim-2.30.0 GO-terms Semantic Similarity Measures
- GOstats-2.70.0 Tools for manipulating GO and microarrays
- GSA-1.03.3 Gene Set Analysis
- GSEABase-1.66.0 Gene set enrichment data structures and methods
- GSVA-1.52.2 Gene Set Variation Analysis for Microarray and RNA-Seq Data
- GWASExactHW-1.2 Exact Hardy-Weinburg Testing for Genome Wide Association Studies
- GWASTools-1.50.0 Tools for Genome Wide Association Studies
- GenomeInfoDb-1.40.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
- GenomeInfoDbData-1.2.12 Species and taxonomy ID look up tables used by GenomeInfoDb
- GenomicAlignments-1.40.0 Representation and manipulation of short genomic alignments
- GenomicFeatures-1.56.0 Conveniently import and query gene models
- GenomicFiles-1.40.0 Distributed computing by file or by range
- GenomicRanges-1.56.0 Representation and manipulation of genomic intervals
- GetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable Interpolation
- Glimma-2.14.0 Interactive visualizations for gene expression analysis
- GlobalOptions-0.1.2 Generate Functions to Get or Set Global Options
- Gmisc-3.0.3 Descriptive Statistics, Transition Plots, and More
- GreyListChIP-1.36.0 Grey Lists – Mask Artefact Regions Based on ChIP Inputs
- Gviz-1.48.0 Plotting data and annotation information along genomic coordinates
- HDF5Array-1.32.0 HDF5 backend for DelayedArray objects
- HDO.db-0.99.1 A set of annotation maps describing the entire Human Disease Ontology
- HMMcopy-1.46.0 Copy number prediction with correction for GC and mappability bias for HTS data
- HSMMSingleCell-1.24.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
- HaploSim-1.8.4.2 Functions to Simulate Haplotypes
- Hmisc-5.1-2 Harrell Miscellaneous
- Homo.sapiens-1.3.1 Annotation package for the Homo.sapiens object
- IDPmisc-1.1.21 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’
- IHW-1.32.0 Independent Hypothesis Weighting
- IRanges-2.38.0 Foundation of integer range manipulation in Bioconductor
- IRdisplay-1.1 ‘Jupyter’ Display Machinery
- IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
- InteractionSet-1.32.0 Base Classes for Storing Genomic Interaction Data
- KEGGREST-1.44.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
- KEGGgraph-1.64.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
- LogicReg-1.6.6 Logic Regression
- LymphoSeq-1.32.0 Analyze high-throughput sequencing of T and B cell receptors
- LymphoSeqDB-0.99.2 LymphoSeq annotation databases
- MAGeCKFlute-2.8.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
- MAST-1.30.0 Model-based Analysis of Single Cell Transcriptomics
- MCMCglmm-2.36 MCMC Generalised Linear Mixed Models
- MPV-1.63 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-1.16.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
- MatrixModels-0.5-3 Modelling with Sparse and Dense Matrices
- Mfuzz-2.64.0 Soft clustering of time series gene expression data
- NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
- NOISeq-2.48.0 Exploratory analysis and differential expression for RNA-seq data
- Nozzle.R1-1.1-1.1 Nozzle Reports
- OrganismDbi-1.46.0 Software to enable the smooth interfacing of different database packages
- PBSddesolve-1.13.4 Solver for Delay Differential Equations
- PFAM.db-3.19.1 A set of protein ID mappings for PFAM
- PICS-2.48.0 Probabilistic inference of ChIP-seq
- PolynomF-2.0-8 Polynomials in R
- ProtGenerics-1.36.0 Generic infrastructure for Bioconductor mass spectrometry packages
- QUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix Estimation
- QuickJSR-1.1.3 Interface for the ‘QuickJS’ Lightweight ‘JavaScript’ Engine
- R.methodsS3-1.8.2 S3 Methods Simplified
- R.oo-1.26.0 R Object-Oriented Programming with or without References
- R.utils-2.12.3 Various Programming Utilities
- R2WinBUGS-2.1-22.1 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
- R2jags-0.8-5 Using R to Run ‘JAGS’
- RBGL-1.80.0 An interface to the BOOST graph library
- RCurl-1.98-1.14 General Network (HTTP/FTP/…) Client Interface for R
- REDCapR-1.1.0 Interaction Between R and REDCap
- RLRsim-3.1-8 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models
- RNASeqPower-1.44.0 Sample size for RNAseq studies
- ROCR-1.0-11 Visualizing the Performance of Scoring Classifiers
- RPresto-1.4.6 DBI Connector to Presto
- RProtoBuf-0.4.22 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)
- RProtoBufLib-2.16.0 C++ headers and static libraries of Protocol buffers
- RSQLite-2.3.6 SQLite Interface for R
- RSclient-0.7-10 Client for Rserve
- RSpectra-0.16-1 Solvers for Large-Scale Eigenvalue and SVD Problems
- RVenn-1.1.0 Set Operations for Many Sets
- RaggedExperiment-1.28.0 Representation of Sparse Experiments and Assays Across Samples
- RcppAnnoy-0.0.22 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
Neighbors
- RcppArmadillo-0.12.8.3.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
Library
- RcppCCTZ-0.2.12 ‘Rcpp’ Bindings for the ‘CCTZ’ Library
- RcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time Functionality
- RcppEigen-0.3.4.0.0 ‘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
- RcppNumerical-0.6-0 ‘Rcpp’ Integration for Numerical Computing Libraries
- RcppParallel-5.1.7 Parallel Programming Tools for ‘Rcpp’
- RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R
Packages
- 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 Update and Manipulate Rd Documentation Objects
- Rdsdp-1.0.5.2.1 R Interface to DSDP Semidefinite Programming Library
- ReportingTools-2.44.0 Tools for making reports in various formats
- Rfast-2.1.0 A Collection of Efficient and Extremely Fast R Functions
- Rgraphviz-2.48.0 Provides plotting capabilities for R graph objects
- Rhdf5lib-1.26.0 hdf5 library as an R package
- Rhpc-0.21-247 Permits *apply() Style Dispatch for ‘HPC’
- RhpcBLASctl-0.23-42 Control the Number of Threads on ‘BLAS’
- Rhtslib-3.0.0 HTSlib high-throughput sequencing library as an R package
- Ringo 1.66.0 [CRAN]
- Rlabkey-3.2.1 Data Exchange Between R and ‘LabKey’ Server
- Rmpfr-0.9-5 R MPFR - Multiple Precision Floating-Point Reliable
- Rmpi-0.7-2 Interface (Wrapper) to MPI (Message-Passing Interface)
- Rsamtools-2.20.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
- Rsubread-2.18.0 Mapping, quantification and variant analysis of sequencing data
- Rtsne-0.17 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
Implementation
- S4Arrays-1.4.0 Foundation of array-like containers in Bioconductor
- S4Vectors-0.42.0 Foundation of vector-like and list-like containers in Bioconductor
- SNPRelate-1.38.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
- SNPassoc-2.1-0 SNPs-Based Whole Genome Association Studies
- SPIA-2.56.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
- ScaledMatrix-1.12.0 Creating a DelayedMatrix of Scaled and Centered Values
- SemiPar-1.0-4.2 Semiparametic Regression
- ShortRead-1.62.0 FASTQ input and manipulation
- SingleCellExperiment-1.26.0 S4 Classes for Single Cell Data
- SparseArray-1.4.3 High-performance sparse data representation and manipulation in R
- SparseM-1.81 Sparse Linear Algebra
- SpatialExperiment-1.14.0 S4 Class for Spatially Resolved -omics Data
- StanHeaders-2.32.7 C++ Header Files for Stan
- SummarizedExperiment-1.34.0 SummarizedExperiment container
- SuperLearner-2.0-29 Super Learner Prediction
- TFBSTools-1.42.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
- TFMPvalue-0.0.9 Efficient and Accurate P-Value Computation for Position Weight
Matrices
- TH.data-1.1-2 TH’s Data Archive
- TitanCNA-1.42.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
- TxDb.Celegans.UCSC.ce6.ensGene-3.2.2 Annotation package for TxDb object(s)
- TxDb.Dmelanogaster.UCSC.dm3.ensGene-3.2.2 Annotation package for TxDb object(s)
- TxDb.Hsapiens.UCSC.hg18.knownGene-3.2.2 Annotation package for TxDb object(s)
- TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)
- TxDb.Mmusculus.UCSC.mm10.knownGene-3.10.0 Annotation package for TxDb object(s)
- TxDb.Mmusculus.UCSC.mm9.knownGene-3.2.2 Annotation package for TxDb object(s)
- TxDb.Rnorvegicus.UCSC.rn4.ensGene-3.2.2 Annotation package for TxDb object(s)
- UCSC.utils-1.0.0 Low-level utilities to retrieve data from the UCSC Genome Browser
- UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
- V8-4.4.2 Embedded JavaScript and WebAssembly Engine for R
- VariantAnnotation-1.50.0 Annotation of Genetic Variants
- VennDiagram-1.7.3 Generate High-Resolution Venn and Euler Plots
- Wrench-1.22.0 Wrench normalization for sparse count data
- XML-3.99-0.16.1 Tools for Parsing and Generating XML Within R and S-Plus
- XVector-0.44.0 Foundation of external vector representation and manipulation in Bioconductor
- abind-1.4-5 Combine Multidimensional Arrays
- ade4-1.7-22 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
- admisc-0.35 Adrian Dusa’s Miscellaneous
- affxparser-1.76.0 Affymetrix File Parsing SDK
- affy-1.82.0 Methods for Affymetrix Oligonucleotide Arrays
- affycoretools-1.76.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
- affyio-1.74.0 Tools for parsing Affymetrix data files
- alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
- amap-0.8-19 Another Multidimensional Analysis Package
- annaffy-1.76.0 Annotation tools for Affymetrix biological metadata
- annotate-1.82.0 Annotation for microarrays
- ape-5.8 Analyses of Phylogenetics and Evolution
- apeglm-1.26.0 Approximate posterior estimation for GLM coefficients
- aplot-0.2.2 Decorate a ‘ggplot’ with Associated Information
- argparser-0.7.2 Command-Line Argument Parser
- arsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical
Summaries
- arules-1.7-7 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
- assertthat-0.2.1 Easy Pre and Post Assertions
- 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-1.36.0 Extract read count signals from bam files
- base64-2.0.1 Base64 Encoder and Decoder
- base64url-1.4 Fast and URL-Safe Base64 Encoder and Decoder
- basilisk-1.16.0 Freezing Python Dependencies Inside Bioconductor Packages
- basilisk.utils-1.16.0 Basilisk Installation Utilities
- batchtools-0.9.17 Tools for Computation on Batch Systems
- bayesplot-1.11.1 Plotting for Bayesian Models
- bbmle-1.0.25.1 Tools for General Maximum Likelihood Estimation
- bdsmatrix-1.3-7 Routines for Block Diagonal Symmetric Matrices
- beachmat-2.20.0 Compiling Bioconductor to Handle Each Matrix Type
- beanplot-1.3.1 Visualization via Beanplots (Like Boxplot/Stripchart/Violin
Plot)
- beeswarm-0.4.0 The Bee Swarm Plot, an Alternative to Stripchart
- benchmark-0.3-6 Benchmark Experiments Toolbox
- bezier-1.1.2 Toolkit for Bezier Curves and Splines
- biglm-0.9-2.1 Bounded Memory Linear and Generalized Linear Models
- biomaRt-2.60.0 Interface to BioMart databases (i.e. Ensembl)
- biomformat-1.32.0 An interface package for the BIOM file format
- biovizBase-1.52.0 Basic graphic utilities for visualization of genomic data.
- bitops-1.0-7 Bitwise Operations
- bookdown-0.39 Authoring Books and Technical Documents with R Markdown
- boot-1.3-30 Bootstrap Functions (Originally by Angelo Canty for S)
- breakaway-4.8.4 Species Richness Estimation and Modeling
- brglm-0.7.2 Bias Reduction in Binomial-Response Generalized Linear Models
- broom.helpers-1.15.0 Helpers for Model Coefficients Tibbles
- bumphunter-1.46.0 Bump Hunter
- caTools-1.18.2 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
- car-3.1-2 Companion to Applied Regression
- carData-3.0-5 Companion to Applied Regression Data Sets
- catdata-1.2.4 Categorical Data
- checkmate-2.3.1 Fast and Versatile Argument Checks
- chipseq-1.54.0 chipseq: A package for analyzing chipseq data
- chromVAR-1.26.0 Chromatin Variation Across Regions
- chron-2.3-61 Chronological Objects which Can Handle Dates and Times
- circlize-0.4.16 Circular Visualization
- classInt-0.4-10 Choose Univariate Class Intervals
- clue-0.3-65 Cluster Ensembles
- cluster-2.1.6 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et
al.
- clusterProfiler-4.12.0 A universal enrichment tool for interpreting omics data
- coda-0.19-4.1 Output Analysis and Diagnostics for MCMC
- colorRamps-2.3.4 Builds Color Tables
- colourpicker-1.3.0 A Colour Picker Tool for Shiny and for Selecting Colours in
Plots
- compare-0.2-6 Comparing Objects for Differences
- config-0.3.2 Manage Environment Specific Configuration Values
- copula-1.1-3 Multivariate Dependence with Copulas
- corpcor-1.6.10 Efficient Estimation of Covariance and (Partial) Correlation
- corrplot-0.92 Visualization of a Correlation Matrix
- cowplot-1.1.3 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
- crosstalk-1.2.1 Inter-Widget Interactivity for HTML Widgets
- crul-1.4.2 HTTP Client
- cubature-2.1.0 Adaptive Multivariate Integration over Hypercubes
- cummeRbund-2.46.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
- curry-0.1.1 Partial Function Application with %<%, %-<%, and %><%
- cvAUC-1.1.4 Cross-Validated Area Under the ROC Curve Confidence Intervals
- cyclocomp-1.1.1 Cyclomatic Complexity of R Code
- cytolib-2.16.0 C++ infrastructure for representing and interacting with the gated cytometry data
- dada2-1.32.0 Accurate, high-resolution sample inference from amplicon sequencing data
- dbscan-1.1-12 Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
- deSolve-1.40 Solvers for Initial Value Problems of Differential Equations
(‘ODE’, ‘DAE’, ‘DDE’)
- degreenet-1.3-5 Models for Skewed Count Distributions Relevant to Networks
- deldir-2.0-4 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
- densvis-1.14.0 Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
- depmap-1.18.0 Cancer Dependency Map Data Package
- derfinder-1.38.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
- derfinderHelper-1.38.0 derfinder helper package
- descr-1.1.8 Descriptive Statistics
- dfoptim-2023.1.0 Derivative-Free Optimization
- diamonds-1.0-5 Analysis and sampling grids from diamond partitions
- dichromat-2.0-0.1 Color Schemes for Dichromats
- diffusionMap-1.2.0 Diffusion Map
- dir.expiry-1.12.0 Managing Expiration for Cache Directories
- directlabels-2024.1.21 Direct Labels for Multicolor Plots
- distributional-0.4.0 Vectorised Probability Distributions
- doBy-4.6.21 Groupwise Statistics, LSmeans, Linear Estimates, Utilities
- doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
- doParallel-1.0.17 Foreach Parallel Adaptor for the ‘parallel’ Package
- doRNG-1.8.6 Generic Reproducible Parallel Backend for ‘foreach’ Loops
- downloader-0.4 Download Files over HTTP and HTTPS
- dqrng-0.4.0 Fast Pseudo Random Number Generators
- drc-3.0-1 Analysis of Dose-Response Curves
- dygraphs-1.1.1.6 Interface to ‘Dygraphs’ Interactive Time Series Charting Library
- e1071-1.7-14 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
- edgeR-4.2.0 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
- ellipse-0.5.0 Functions for Drawing Ellipses and Ellipse-Like Confidence
Regions
- emdbook-1.3.13 Support Functions and Data for “Ecological Models and Data”
- enrichplot-1.24.0 Visualization of Functional Enrichment Result
- ensembldb-2.28.0 Utilities to create and use Ensembl-based annotation databases
- epitools-0.5-10.1 Epidemiology Tools
- ergm-4.6.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks
- ergm.ego-1.1.0 Fit, Simulate and Diagnose Exponential-Family Random Graph
Models to Egocentrically Sampled Network Data
- ergm.multi-0.2.1 Fit, Simulate and Diagnose Exponential-Family Models for
Multiple or Multilayer Networks
- 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-1.0.8 Functions and Datasets for Books by Julian Faraway
- fastcluster-1.2.6 Fast Hierarchical Clustering Routines for R and ‘Python’
- fastmatch-1.1-4 Fast ‘match()’ Function
- fastseg-1.50.0 fastseg - a fast segmentation algorithm
- fasttime-1.1-0 Fast Utility Function for Time Parsing and Conversion
- fda-6.1.8 Functional Data Analysis
- fdrtool-1.2.17 Estimation of (Local) False Discovery Rates and Higher Criticism
- fds-1.8 Functional Data Sets
- ff-4.0.12 Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
- fftwtools-0.9-11 Wrapper for ‘FFTW3’ Includes: One-Dimensional, Two-Dimensional,
Three-Dimensional, and Multivariate Transforms
- fgsea-1.30.0 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-3.42.0 Clustering for Flow Cytometry
- flowCore-2.16.0 flowCore: Basic structures for flow cytometry data
- flowStats-4.16.0 Statistical methods for the analysis of flow cytometry data
- flowViz-1.68.0 Visualization for flow cytometry
- flowWorkspace-4.16.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
- fontBitstreamVera-0.1.1 Fonts with ‘Bitstream Vera Fonts’ License
- fontLiberation-0.1.0 Liberation Fonts
- fontquiver-0.2.1 Set of Installed Fonts
- foreign-0.8-86 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’,
‘Systat’, ‘Weka’, ‘dBase’, …
- forestplot-3.1.3 Advanced Forest Plot Using ‘grid’ Graphics
- forge-0.2.0 Casting Values into Shape
- formatR-1.14 Format R Code Automatically
- formula.tools-1.7.1 Programmatic Utilities for Manipulating Formulas, Expressions,
Calls, Assignments and Other R Objects
- fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
- futile.logger-1.4.3 A Logging Utility for R
- futile.options-1.0.1 Futile Options Management
- gage-2.54.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
- gam-1.22-3 Generalized Additive Models
- gamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
- gcrma-2.76.0 Background Adjustment Using Sequence Information
- gdsfmt-1.40.0
- gdtools-0.3.7 Utilities for Graphical Rendering and Fonts Management
- geneLenDataBase-1.39.0 Lengths of mRNA transcripts for a number of genomes
- genefilter-1.86.0 genefilter: methods for filtering genes from high-throughput experiments
- geneplotter-1.82.0 Graphics related functions for Bioconductor
- gfonts-0.2.0 Offline ‘Google’ Fonts for ‘Markdown’ and ‘Shiny’
- ggVennDiagram-1.5.2 A ‘ggplot2’ Implement of Venn Diagram
- ggbeeswarm-0.7.2 Categorical Scatter (Violin Point) Plots
- ggbio-1.52.0 Visualization tools for genomic data
- ggcyto-1.32.0 Visualize Cytometry data with ggplot
- ggdendro-0.2.0 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
- ggforce-0.4.2 Accelerating ‘ggplot2’
- ggfun-0.1.4 Miscellaneous Functions for ‘ggplot2’
- ggnewscale-0.4.10 Multiple Fill and Colour Scales in ‘ggplot2’
- 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-0.9.5 Automatically Position Non-Overlapping Text Labels with
‘ggplot2’
- ggridges-0.5.6 Ridgeline Plots in ‘ggplot2’
- ggsci-3.0.3 Scientific Journal and Sci-Fi Themed Color Palettes for
‘ggplot2’
- ggsignif-0.6.4 Significance Brackets for ‘ggplot2’
- ggstats-0.6.0 Extension to ‘ggplot2’ for Plotting Stats
- ggthemes-5.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’
- ggtree-3.12.0 an R package for visualization of tree and annotation data
- glmnet-4.1-8 Lasso and Elastic-Net Regularized Generalized Linear Models
- glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Model
- gmp-0.7-4 Multiple Precision Arithmetic
- goftest-1.2-3 Classical Goodness-of-Fit Tests for Univariate Distributions
- gplots-3.1.3.1 Various R Programming Tools for Plotting Data
- graph-1.82.0 graph: A package to handle graph data structures
- graphlayouts-1.1.1 Additional Layout Algorithms for Network Visualizations
- gridExtra-2.3 Miscellaneous Functions for “Grid” Graphics
- gridGraphics-0.5-1 Redraw Base Graphics Using ‘grid’ Graphics
- grpreg-3.4.0 Regularization Paths for Regression Models with Grouped
Covariates
- gsl-2.1-8 Wrapper for the Gnu Scientific Library
- gson-0.1.0 Base Class and Methods for ‘gson’ Format
- gsubfn-0.7 Utilities for Strings and Function Arguments
- gtools-3.9.5 Various R Programming Tools
- hapassoc-1.2-9 Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm
- haplo.stats-1.9.5.1 Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
- hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
- here-1.0.1 A Simpler Way to Find Your Files
- hexbin-1.28.3 Hexagonal Binning Routines
- hgu133plus2.db-3.13.0 Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)
- hopach-2.64.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
- htmlTable-2.4.2 Advanced Tables for Markdown/HTML
- httpcode-0.3.0 ‘HTTP’ Status Code Helper
- hwriter-1.3.2.1 HTML Writer - Outputs R Objects in HTML Format
- 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-0.46.0 Parsing Illumina Microarray Output Files
- impute-1.78.0 impute: Imputation for microarray data
- ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
- inferference-1.0.2 Methods for Causal Inference with Interference
- inline-0.3.19 Functions to Inline C, C++, Fortran Function Calls from R
- interactiveDisplayBase-1.42.0 Base package for enabling powerful shiny web displays of Bioconductor objects
- interp-1.1-6 Interpolation Methods
- invgamma-1.1 The Inverse Gamma Distribution
- iotools-0.3-5 I/O Tools for Streaming
- irlba-2.3.5.1 Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
- its-1.1.8 Irregular Time Series
- jomo-2.7-6 Multilevel Joint Modelling Multiple Imputation
- jpeg-0.1-10 Read and write JPEG images
- karyoploteR-1.30.0 Plot customizable linear genomes displaying arbitrary data
- kernlab-0.9-32 Kernel-Based Machine Learning Lab
- 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
- ks-1.14.2 Kernel Smoothing
- kyotil-2024.5-8 Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
- labelled-2.13.0 Manipulating Labelled Data
- lambda.r-1.2.4 Modeling Data with Functional Programming
- lars-1.3 Least Angle Regression, Lasso and Forward Stagewise
- latentnet-2.11.0 Latent Position and Cluster Models for Statistical Networks
- latticeExtra-0.6-30 Extra Graphical Utilities Based on Lattice
- lazyeval-0.2.2 Lazy (Non-Standard) Evaluation
- lgr-0.4.4 A Fully Featured Logging Framework
- limma-3.60.0 Linear Models for Microarray Data
- lintr-3.1.2 A ‘Linter’ for R Code
- lme4-1.1-35.3 Linear Mixed-Effects Models using ‘Eigen’ and S4
- lmtest-0.9-40 Testing Linear Regression Models
- locfit-1.5-9.9 Local Regression, Likelihood and Density Estimation
- logistf-1.26.0 Firth’s Bias-Reduced Logistic Regression
- logspline-2.1.22 Routines for Logspline Density Estimation
- lokern-1.1-11 Kernel Regression Smoothing with Local or Global Plug-in
Bandwidth
- loo-2.7.0 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
- lpSolveAPI-5.5.2.0-17.11 R Interface to ‘lp_solve’ Version 5.5.2.0
- lpridge-1.1-0 Local Polynomial (Ridge) Regression
- lpsymphony-1.32.0 Symphony integer linear programming solver in R
- lumi-2.56.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
- maSigPro-1.76.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
- magic-1.6-1 Create and Investigate Magic Squares
- magick-2.8.3 Advanced Graphics and Image-Processing in R
- mapdata-2.3.1 Extra Map Databases
- maps-3.4.2 Draw Geographical Maps
- markdown-1.12 Render Markdown with ‘commonmark’
- marray-1.82.0 Exploratory analysis for two-color spotted microarray data
- matrixStats-1.3.0 Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
- mclust-6.1.1 Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
- metagenomeSeq-1.46.0 Statistical analysis for sparse high-throughput sequencing
- methylKit-1.30.0 DNA methylation analysis from high-throughput bisulfite sequencing results
- methylumi-2.50.0 Handle Illumina methylation data
- mice-3.16.0 Multivariate Imputation by Chained Equations
- microbenchmark-1.4.10 Accurate Timing Functions
- minfi-1.50.0 Analyze Illumina Infinium DNA methylation arrays
- minqa-1.2.6 Derivative-Free Optimization Algorithms by Quadratic
Approximation
- misc3d-0.9-1 Miscellaneous 3D Plots
- mitml-0.4-5 Tools for Multiple Imputation in Multilevel Modeling
- mitools-2.4 Tools for Multiple Imputation of Missing Data
- mixOmics-6.28.0 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
- mnormt-2.1.1 The Multivariate Normal and t Distributions, and Their Truncated
Versions
- mondate-1.0 Keep Track of Dates in Terms of Months
- motifmatchr-1.26.0 Fast Motif Matching in R
- msa-1.36.0 Multiple Sequence Alignment
- msigdbr-7.5.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
- multcomp-1.4-25 Simultaneous Inference in General Parametric Models
- multicool-1.0.1 Permutations of Multisets in Cool-Lex Order
- multtest-2.60.0 Resampling-based multiple hypothesis testing
- mvtnorm-1.2-4 Multivariate Normal and t Distributions
- nabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low
Dimensions
- nanotime-0.3.7 Nanosecond-Resolution Time Support for R
- ncdfFlow-2.50.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
- network-1.18.2 Classes for Relational Data
- networkDynamic-0.11.4 Dynamic Extensions for Network Objects
- networkLite-1.0.5 An Simplified Implementation of the ‘network’ Package
Functionality
- networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Sampling
- nleqslv-3.3.5 Solve Systems of Nonlinear Equations
- nloptr-2.0.3 R Interface to NLopt
- nnls-1.5 The Lawson-Hanson Algorithm for Non-Negative Least Squares
(NNLS)
- nor1mix-1.3-3 Normal aka Gaussian 1-d Mixture Models
- numbers-0.8-5 Number-Theoretic Functions
- nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
- odbc-1.4.2 Connect to ODBC Compatible Databases (using the DBI Interface)
- oligo-1.68.0 Preprocessing tools for oligonucleotide arrays
- oligoClasses-1.66.0 Classes for high-throughput arrays supported by oligo and crlmm
- openCyto-2.16.0 Hierarchical Gating Pipeline for flow cytometry data
- openxlsx-4.2.5.2 Read, Write and Edit xlsx Files
- operator.tools-1.6.3 Utilities for Working with R’s Operators
- ordinal-2023.12-4 Regression Models for Ordinal Data
- org.Hs.eg.db-3.19.1 Genome wide annotation for Human
- org.Mm.eg.db-3.19.1 Genome wide annotation for Mouse
- osqp-0.6.3.2 Quadratic Programming Solver using the ‘OSQP’ Library
- pROC-1.18.5 Display and Analyze ROC Curves
- pack-0.1-1 Convert values to/from raw vectors
- pan-1.9 Multiple Imputation for Multivariate Panel or Clustered Data
- partools-1.1.6 Tools for the ‘Parallel’ Package
- pathview-1.44.0 a tool set for pathway based data integration and visualization
- pbapply-1.7-2 Adding Progress Bar to ‘*apply’ Functions
- pbkrtest-0.5.2 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
Methods for Test in Mixed Models
- pbs-1.1 Periodic B Splines
- pcaMethods-1.96.0 A collection of PCA methods
- pcaPP-2.0-4 Robust PCA by Projection Pursuit
- pdftools-3.4.0 Text Extraction, Rendering and Converting of PDF Documents
- pdist-1.2.1 Partitioned Distance Function
- pedigree-1.4.2 Pedigree Functions
- pedigreemm-0.3-4 Pedigree-Based Mixed-Effects Models
- perm-1.0-0.4 Exact or Asymptotic Permutation Tests
- permute-0.9-7 Functions for Generating Restricted Permutations of Data
- phangorn-2.11.1 Phylogenetic Reconstruction and Analysis
- pheatmap-1.0.12 Pretty Heatmaps
- phyloseq-1.48.0 Handling and analysis of high-throughput microbiome census data
- pixmap-0.4-13 Bitmap Images / Pixel Maps
- plogr-0.2.0 The ‘plog’ C++ Logging Library
- plot3D-1.4.1 Plotting Multi-Dimensional Data
- plotly-4.10.4 Create Interactive Web Graphics via ‘plotly.js’
- plotrix-3.8-4 Various Plotting Functions
- plyr-1.8.9 Tools for Splitting, Applying and Combining Data
- png-0.1-8 Read and write PNG images
- poisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distribution
- polspline-1.1.25 Polynomial Spline Routines
- polyclip-1.10-6 Polygon Clipping
- polyester-1.39.0 Simulate RNA-seq reads
- polynom-1.4-1 A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulations
- polyreg-0.8.0 Polynomial Regression
- posterior-1.5.0 Tools for Working with Posterior Distributions
- poweRlaw-0.80.0 Analysis of Heavy Tailed Distributions
- pracma-2.4.4 Practical Numerical Math Functions
- premessa 0.3.4 [CRAN]
- preprocessCore-1.66.0 A collection of pre-processing functions
- profileModel-0.6.1 Profiling Inference Functions for Various Model Classes
- proto-1.0.0 Prototype Object-Based Programming
- proxy-0.4-27 Distance and Similarity Measures
- pspline-1.0-19 Penalized Smoothing Splines
- psychotools-0.7-4 Psychometric Modeling Infrastructure
- pwalign-1.0.0 Perform pairwise sequence alignments
- qdapRegex-0.7.8 Regular Expression Removal, Extraction, and Replacement Tools
- qpdf-1.3.3 Split, Combine and Compress PDF Files
- qqconf-1.3.2 Creates Simultaneous Testing Bands for QQ-Plots
- qtl-1.66 Tools for Analyzing QTL Experiments
- quadprog-1.5-8 Functions to Solve Quadratic Programming Problems
- quantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimes
- quantreg-5.97 Quantile Regression
- quantsmooth-1.70.0 Quantile smoothing and genomic visualization of array data
- qvalue-2.36.0 Q-value estimation for false discovery rate control
- qvcalc-1.0.3 Quasi Variances for Factor Effects in Statistical Models
- r2d3-0.2.6 Interface to ‘D3’ Visualizations
- rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
- rGADEM-2.52.0 de novo motif discovery
- rainbow-3.8 Bagplots, Boxplots and Rainbow Plots for Functional Data
- randomForest-4.7-1.1 Breiman and Cutler’s Random Forests for Classification and
Regression
- rbenchmark-1.0.0 Benchmarking routine for R
- rbibutils-2.2.16 Read ‘Bibtex’ Files and Convert Between Bibliography Formats
- refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from
‘Ensembl’ and ‘UCSC’ Genome Browsers
- refund-0.1-35 Regression with Functional Data
- regioneR-1.36.0 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-0.6-13 Data Structures and Algorithms for Relations
- relevent-1.2-1 Relational Event Models
- repr-1.1.7 Serializable Representations
- 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-1.36.1 Interface to ‘Python’
- rex-1.2.1 Friendly Regular Expressions
- rgenoud-5.9-0.10 R Version of GENetic Optimization Using Derivatives
- rhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Library
- rhdf5-2.48.0 R Interface to HDF5
- rhdf5filters-1.16.0 HDF5 Compression Filters
- rjags-4-15 Bayesian Graphical Models using MCMC
- rje-1.12.1 Miscellaneous Useful Functions for Statistics
- rjson-0.2.21 JSON for R
- rle-0.9.2 Common Functions for Run-Length Encoded Vectors
- rms-6.8-0 Regression Modeling Strategies
- rngtools-1.5.2 Utility Functions for Working with Random Number Generators
- robustbase-0.99-2 Basic Robust Statistics
- rrcov-1.7-5 Scalable Robust Estimators with High Breakdown Point
- rslurm-0.6.2 Submit R Calculations to a ‘Slurm’ Cluster
- rsparse-0.5.1 Statistical Learning on Sparse Matrices
- rstan-2.32.6 R Interface to Stan
- rstanarm-2.32.1 Bayesian Applied Regression Modeling via Stan
- rstantools-2.4.0 Tools for Developing R Packages Interfacing with ‘Stan’
- rstatix-0.7.2 Pipe-Friendly Framework for Basic Statistical Tests
- rsvd-1.0.5 Randomized Singular Value Decomposition
- rtracklayer-1.64.0 R interface to genome annotation files and the UCSC genome browser
- rvcheck-0.2.1 R/Package Version Check
- rzmq-0.9.13 R Bindings for ‘ZeroMQ’
- s2-1.1.6 Spherical Geometry Operators Using the S2 Geometry Library
- samr-3.0 SAM: Significance Analysis of Microarrays
- sandwich-3.1-0 Robust Covariance Matrix Estimators
- scater-1.32.0 Single-Cell Analysis Toolkit for Gene Expression Data in R
- scattermore-1.2 Scatterplots with More Points
- scatterpie-0.2.2 Scatter Pie Plot
- scatterplot3d-0.3-44 3D Scatter Plot
- 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
- scs-3.2.4 Splitting Conic Solver
- scuttle-1.14.0 Single-Cell RNA-Seq Analysis Utilities
- seqLogo-1.70.0 Sequence logos for DNA sequence alignments
- seqminer-9.4 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
- sf-1.0-16 Simple Features for R
- sfsmisc-1.1-18 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
- shadowtext-0.1.3 Shadow Text Grob and Layer
- shinyBS-0.61.1 Twitter Bootstrap Components for Shiny
- shinyFiles-0.9.3 A Server-Side File System Viewer for Shiny
- shinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s
Recalculating
- shinyjqui-0.4.1 ‘jQuery UI’ Interactions and Effects for Shiny
- shinyjs-2.1.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
- shinystan-2.6.0 Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
- shinythemes-1.2.0 Themes for Shiny
- siggenes-1.78.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
- sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header
Files
- slam-0.1-50 Sparse Lightweight Arrays and Matrices
- sna-2.7-2 Tools for Social Network Analysis
- snow-0.4-4 Simple Network of Workstations
- snpStats-1.54.0 SnpMatrix and XSnpMatrix classes and methods
- sodium-1.3.1 A Modern and Easy-to-Use Crypto Library
- sp-2.1-4 Classes and Methods for Spatial Data
- sparklyr-1.8.6 R Interface to Apache Spark
- sparseMatrixStats-1.16.0 Summary Statistics for Rows and Columns of Sparse Matrices
- spatstat-3.0-8 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
- spatstat.data-3.0-4 Datasets for ‘spatstat’ Family
- spatstat.explore-3.2-7 Exploratory Data Analysis for the ‘spatstat’ Family
- spatstat.geom-3.2-9 Geometrical Functionality of the ‘spatstat’ Family
- spatstat.linnet-3.1-5 Linear Networks Functionality of the ‘spatstat’ Family
- spatstat.model-3.2-11 Parametric Statistical Modelling and Inference for the
‘spatstat’ Family
- spatstat.random-3.2-3 Random Generation Functionality for the ‘spatstat’ Family
- spatstat.sparse-3.0-3 Sparse Three-Dimensional Arrays and Linear Algebra Utilities
- spatstat.utils-3.0-4 Utility Functions for ‘spatstat’
- sqldf-0.4-11 Manipulate R Data Frames Using SQL
- squash-1.0.9 Color-Based Plots for Multivariate Visualization
- srvyr-1.2.0 ‘dplyr’-Like Syntax for Summary Statistics of Survey Data
- ssgraph-1.15 Bayesian Graph Structure Learning using Spike-and-Slab Priors
- stabledist-0.7-1 Stable Distribution Functions
- statmod-1.5.0 Statistical Modeling
- statnet.common-4.9.0 Common R Scripts and Utilities Used by the Statnet Project
Software
- stringdist-0.9.12 Approximate String Matching, Fuzzy Text Search, and String
Distance Functions
- strucchange-1.5-3 Testing, Monitoring, and Dating Structural Changes
- survey-4.4-2 Analysis of Complex Survey Samples
- sva-3.52.0 Surrogate Variable Analysis
- systemPipeR-2.10.0 systemPipeR: workflow management and report generation environment
- tables-0.9.25 Formula-Driven Table Generation
- tensor-1.5 Tensor product of arrays
- tensorA-0.36.2.1 Advanced Tensor Arithmetic with Named Indices
- tergm-4.2.0 Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
- tergmLite-2.6.1 Fast Simulation of Simple Temporal Exponential Random Graph
Models
- text2vec-0.6.4 Modern Text Mining Framework for R
- threejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globes
- tidyposterior-1.0.1 Bayesian Analysis to Compare Models using Resampling Statistics
- tidytree-0.4.6 A Tidy Tool for Phylogenetic Tree Data Manipulation
- tiff-0.1-12 Read and Write TIFF Images
- tilingArray-1.82.0 Transcript mapping with high-density oligonucleotide tiling arrays
- timeSeries-4032.109 Financial Time Series Objects (Rmetrics)
- tkWidgets-1.82.0 R based tk widgets
- treeio-1.28.0 Base Classes and Functions for Phylogenetic Tree Input and Output
- triebeard-0.4.1 ‘Radix’ Trees in ‘Rcpp’
- truncnorm-1.0-9 Truncated Normal Distribution
- trust-0.1-8 Trust Region Optimization
- tweenr-2.0.3 Interpolate Data for Smooth Animations
- txdbmaker-1.0.0 Tools for making TxDb objects from genomic annotations
- ucminf-1.2.1 General-Purpose Unconstrained Non-Linear Optimization
- udunits2-0.13.2.1 Udunits-2 Bindings for R
- units-0.8-5 Measurement Units for R Vectors
- universalmotif-1.22.0 Import, Modify, and Export Motifs with R
- urltools-1.7.3 Vectorised Tools for URL Handling and Parsing
- uwot-0.2.2 The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
- vegan-2.6-6 Community Ecology Package
- venn-1.12 Draw Venn Diagrams
- vimp-2.3.3 Perform Inference on Algorithm-Agnostic Variable Importance
- vipor-0.4.7 Plot Categorical Data Using Quasirandom Noise and Density
Estimates
- viridis-0.6.5 Colorblind-Friendly Color Maps for R
- vsn-3.72.0 Variance stabilization and calibration for microarray data
- wavethresh-4.7.2 Wavelets Statistics and Transforms
- webp-1.2.0 A New Format for Lossless and Lossy Image Compression
- widgetTools-1.82.0 Creates an interactive tcltk widget
- wk-0.9.1 Lightweight Well-Known Geometry Parsing
- xCell 1.1.0 [CRAN]
- xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Tree
- xts-0.13.2 eXtensible Time Series
- yulab.utils-0.1.4 Supporting Functions for Packages Maintained by ‘YuLab-SMU’
- zCompositions-1.5.0-3 Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Sets
- zlibbioc-1.50.0 An R packaged zlib-1.2.5
- zoo-1.8-12 S3 Infrastructure for Regular and Irregular Time Series (Z’s
Ordered Observations)