fhR-4.1.2-foss-2020b

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The fhR module contains libraries that have been requested by Hutch users. The Fred Hutch module inherits the modules from the base R module that is maintained by the EasyBuild community. Hutch users should use the fh versions of R.

Known Issues

None

Package List

ADGofTest-0.3 Anderson-Darling GoF test
AICcmodavg-2.3-1 Model Selection and Multimodel Inference Based on (Q)AIC(c)
ALDEx2-1.26.0 Analysis Of Differential Abundance Taking Sample Variation Into Account
ALL-1.36.0 A data package
ASCAT 2.5.2
AUC-0.3.0 Threshold independent performance measures for probabilistic classifiers.
AgiMicroRna-2.44.0 Processing and Differential Expression Analysis of Agilent microRNA chips
AlgDesign-1.2.0 Algorithmic Experimental Design
AnalyzeFMRI-1.1-24 Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format
AnnotationDbi-1.56.2 Manipulation of SQLite-based annotations in Bioconductor
AnnotationFilter-1.18.0 Facilities for Filtering Bioconductor Annotation Resources
AnnotationForge-1.36.0 Tools for building SQLite-based annotation data packages
AnnotationHub-3.2.0 Client to access AnnotationHub resources
ArchR 1.0.1
BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
BBmisc-1.11 Miscellaneous Helper Functions for B. Bischl
BCEE-1.3.0 The Bayesian Causal Effect Estimation Algorithm
BDgraph-2.64 Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
BH-1.75.0-0 Boost C++ Header Files
BIGL-1.6.5 Biochemically Intuitive Generalized Loewe Model
BMA-3.18.15 Bayesian Model Averaging
BSgenome-1.62.0 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)
BatchJobs-1.8 Batch Computing with R
BayesPen-1.0 Bayesian Penalized Credible Regions
BayesianTools-0.1.7 General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Bhat-0.9-10 General likelihood exploration
BiasedUrn-1.07 Biased Urn Model Distributions
Biobase-2.54.0 Biobase: Base functions for Bioconductor
BiocFileCache-2.2.0 Manage Files Across Sessions
BiocGenerics-0.40.0 S4 generic functions used in Bioconductor
BiocIO-1.4.0 Standard Input and Output for Bioconductor Packages
BiocManager-1.30.16 Access the Bioconductor Project Package Repository
BiocNeighbors-1.12.0 Nearest Neighbor Detection for Bioconductor Packages
BiocParallel-1.28.1 Bioconductor facilities for parallel evaluation
BiocSingular-1.10.0 Singular Value Decomposition for Bioconductor Packages
BiocStyle-2.22.0 Standard styles for vignettes and other Bioconductor documents
BiocVersion-3.14.0 Set the appropriate version of Bioconductor packages
Biostrings-2.62.0 Efficient manipulation of biological strings
BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
Bolstad-0.2-41 Functions for Elementary Bayesian Inference
Bolstad2-1.0-28 Bolstad functions
Boruta-7.0.0 Wrapper Algorithm for All Relevant Feature Selection
BradleyTerry2-1.1-2 Bradley-Terry Models
Brobdingnag-1.2-6 Very Large Numbers in R
CATALYST-1.18.0 Cytometry dATa anALYSis Tools
CBPS-0.22 Covariate Balancing Propensity Score
CGHbase-1.54.0 CGHbase: Base functions and classes for arrayCGH data analysis.
CLONETv2-2.2.1 Clonality Estimates in Tumor
CMA-1.52.0 Synthesis of microarray-based classification
CNEr-1.30.0 CNE Detection and Visualization
COMPASS-1.32.0 Combinatorial Polyfunctionality Analysis of Single Cells
CVST-0.2-2 Fast Cross-Validation via Sequential Testing
Cairo-1.5-12.2 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-2.60.0 Category Analysis
ChIPpeakAnno-3.28.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
ChIPseeker-1.30.2 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-2.10.0 Make Complex Heatmaps
ConsensusClusterPlus-1.58.0 ConsensusClusterPlus
CovSel-1.2.1 Model-Free Covariate Selection
CytoML-2.6.0 A GatingML Interface for Cross Platform Cytometry Data Sharing
DAAG-1.24 Data Analysis and Graphics Data and Functions
DBI-1.1.1 R Database Interface
DECIPHER-2.22.0 Tools for curating, analyzing, and manipulating biological sequences
DEGseq-1.48.0 Identify Differentially Expressed Genes from RNA-seq data
DESeq2-1.34.0 Differential gene expression analysis based on the negative binomial distribution
DEoptim-2.2-6 Global Optimization by Differential Evolution
DEoptimR-1.0-9 Differential Evolution Optimization in Pure R
DHARMa-0.4.4 Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
DMCfun-2.0.2 Diffusion Model of Conflict (DMC) in Reaction Time Tasks
DNAcopy-1.68.0 DNA copy number data analysis
DO.db-2.9 A set of annotation maps describing the entire Disease Ontology
DOSE-3.20.1 Disease Ontology Semantic and Enrichment analysis
DOT-0.1 Render and Export DOT Graphs in R
DRR-0.0.4 Dimensionality Reduction via Regression
DT-0.19 A Wrapper of the JavaScript Library ‘DataTables’
DTRreg-1.7 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
DelayedArray-0.20.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
DelayedMatrixStats-1.16.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
Deriv-4.1.3 Symbolic Differentiation
DescTools-0.99.43 Tools for Descriptive Statistics
DiagrammeR-1.0.6.1 Graph/Network Visualization
DiceDesign-1.9 Designs of Computer Experiments
DiceKriging-1.6.0 Kriging Methods for Computer Experiments
DiffBind-3.4.0 Differential Binding Analysis of ChIP-Seq Peak Data
DirichletMultinomial-1.36.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
DistributionUtils-0.6-0 Distribution Utilities
DynDoc-1.72.0 Dynamic document tools
EBImage-4.36.0 Image processing and analysis toolbox for R
ENMeval-2.0.1 Automated Tuning and Evaluations of Ecological Niche Models
EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
EnvStats-2.4.0 Package for Environmental Statistics, Including US EPA Guidance
EpiModel-2.2.0 Mathematical Modeling of Infectious Disease Dynamics
Exact-3.0 Unconditional Exact Test
FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
FME-1.3.6.2 A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis
FNN-1.1.3 Fast Nearest Neighbor Search Algorithms and Applications
FactoMineR-2.4 Multivariate Exploratory Data Analysis and Data Mining
FlowSOM-2.2.0 Using self-organizing maps for visualization and interpretation of cytometry data
Formula-1.2-4 Extended Model Formulas
GENESIS-2.24.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GEOquery-2.62.1 Get data from NCBI Gene Expression Omnibus (GEO)
GGally-2.1.2 Extension to ‘ggplot2’
GO.db-3.14.0 A set of annotation maps describing the entire Gene Ontology
GOSemSim-2.20.0 GO-terms Semantic Similarity Measures
GOstats-2.60.0 Tools for manipulating GO and microarrays
GPfit-1.0-8 Gaussian Processes Modeling
GSA-1.03.1 Gene Set Analysis
GSEABase-1.56.0 Gene set enrichment data structures and methods
GSVA-1.42.0 Gene Set Variation Analysis for microarray and RNA-seq data
GUTS-1.1.1 Fast Calculation of the Likelihood of a Stochastic Survival Model
GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
GWASTools-1.40.0 Tools for Genome Wide Association Studies
GenSA-1.1.7 Generalized Simulated Annealing
GeneNet-1.2.15 Modeling and Inferring Gene Networks
GenomeGraphs 1.46.0
GenomeInfoDb-1.30.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
GenomeInfoDbData-1.2.7 Species and taxonomy ID look up tables used by GenomeInfoDb
GenomicAlignments-1.30.0 Representation and manipulation of short genomic alignments
GenomicFeatures-1.46.1 Conveniently import and query gene models
GenomicFiles-1.30.0 Distributed computing by file or by range
GenomicRanges-1.46.1 Representation and manipulation of genomic intervals
GetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable Interpolation
GillespieSSA-0.6.1 Gillespie’s Stochastic Simulation Algorithm (SSA)
Glimma-2.4.0 Interactive HTML graphics
GlobalOptions-0.1.2 Generate Functions to Get or Set Global Options
Gmisc-2.1.0 Descriptive Statistics, Transition Plots, and More
GreyListChIP-1.26.0 Grey Lists – Mask Artefact Regions Based on ChIP Inputs
Gviz-1.38.0 Plotting data and annotation information along genomic coordinates
GxEScanR-2.0.2 Run GWAS/GWEIS Scans Using Binary Dosage Files
HDF5Array-1.22.1 HDF5 backend for DelayedArray objects
HMMcopy-1.36.0 Copy number prediction with correction for GC and mappability bias for HTS data
HSMMSingleCell-1.14.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
HWxtest-1.1.9 Exact Tests for Hardy-Weinberg Proportions
HaploSim-1.8.4 Functions to simulate haplotypes
HiddenMarkov-1.8-13 Hidden Markov Models
Hmisc-4.6-0 Harrell Miscellaneous
Homo.sapiens-1.3.1 Annotation package for the Homo.sapiens object
IDPmisc-1.1.20 ‘Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)’
IHW-1.22.0 Independent Hypothesis Weighting
IRanges-2.28.0 Foundation of integer range manipulation in Bioconductor
IRdisplay-1.0 ‘Jupyter’ Display Machinery
ISOcodes-2021.02.24 Selected ISO Codes
IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
InteractionSet-1.22.0 Base Classes for Storing Genomic Interaction Data
Iso-0.0-18.1 Functions to Perform Isotonic Regression
JADE-2.0-3 Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria
JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J. Buttlar
KEGGREST-1.34.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
KEGGgraph-1.54.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KODAMA-1.8 Knowledge Discovery by Accuracy Maximization
KernSmooth-2.23-20 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
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
LogicReg-1.6.4 Logic Regression
LymphoSeq-1.22.0 Analyze high-throughput sequencing of T and B cell receptors
LymphoSeqDB-0.99.2 LymphoSeq annotation databases
MAGeCKFlute-1.14.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
MALDIquant-1.20 Quantitative Analysis of Mass Spectrometry Data
MASS-7.3-54 Support Functions and Datasets for Venables and Ripley’s MASS
MAST-1.20.0 Model-based Analysis of Single Cell Transcriptomics
MCMCglmm-2.32 MCMC Generalised Linear Mixed Models
MCMCpack-1.6-0 Markov Chain Monte Carlo (MCMC) Package
MIIVsem-0.5.8 Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
MPV-1.57 Data Sets from Montgomery, Peck and Vining
MatchIt-4.3.0 Nonparametric Preprocessing for Parametric Causal Inference
Matching-4.9-11 Multivariate and Propensity Score Matching with Balance Optimization
Matrix-1.3-4 Sparse and Dense Matrix Classes and Methods
MatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
MatrixGenerics-1.6.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
MatrixModels-0.5-0 Modelling with Sparse and Dense Matrices
Mfuzz-2.54.0 Soft clustering of time series gene expression data
ModelMetrics-1.2.2.2 Rapid Calculation of Model Metrics
NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
NCmisc-1.1.6 Miscellaneous Functions for Creating Adaptive Functions and Scripts
NISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NIST
NLP-0.2-1 Natural Language Processing Infrastructure
NOISeq-2.38.0 Exploratory analysis and differential expression for RNA-seq data
OceanView-1.0.6 Visualisation of Oceanographic Data and Model Output
OrganismDbi-1.36.0 Software to enable the smooth interfacing of different database packages
PBSddesolve-1.12.6 Solver for Delay Differential Equations
PCAmatchR-0.3.0 Match Cases to Controls Based on Genotype Principal Components
PFAM.db-3.14.0 A set of protein ID mappings for PFAM
PICS-2.38.0 Probabilistic inference of ChIP-seq
ParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
PermAlgo-1.1 Permutational Algorithm to Simulate Survival Data
PoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log linear model
PolynomF-2.0-3 Polynomials in R
PresenceAbsence-1.1.9 Presence-Absence Model Evaluation.
ProtGenerics-1.26.0 Generic infrastructure for Bioconductor mass spectrometry packages
QUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix Estimation
R.cache-0.15.0 Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations
R.matlab-3.6.2 Read and Write MAT Files and Call MATLAB from Within R
R.methodsS3-1.8.1 S3 Methods Simplified
R.oo-1.24.0 R Object-Oriented Programming with or without References
R.rsp-0.44.0 Dynamic Generation of Scientific Reports
R.utils-2.11.0 Various Programming Utilities
R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
R2jags-0.7-1 Using R to Run ‘JAGS’
R6-2.5.1 Encapsulated Classes with Reference Semantics
RANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
RBGL-1.70.0 An interface to the BOOST graph library
RCAL-2.0 Regularized Calibrated Estimation
RCircos-1.2.1 Circos 2D Track Plot
RColorBrewer-1.1-2 ColorBrewer Palettes
RCurl-1.98-1.5 General Network (HTTP/FTP/…) Client Interface for R
REDCapR-1.0.0 Interaction Between R and REDCap
RGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation Analysis for Multiblock Data
RInside-0.2.16 C++ Classes to Embed R in C++ (and C) Applications
RItools-0.1-17 Randomization Inference Tools
RJSONIO-1.3-1.6 Serialize R Objects to JSON, JavaScript Object Notation
RLRsim-3.1-6 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models
RMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix Theory
RNASeqPower-1.34.0 Sample size for RNAseq studies
RNeXML-2.4.5 Semantically Rich I/O for the ‘NeXML’ Format
RNifti-1.3.1 Fast R and C++ Access to NIfTI Images
ROCR-1.0-11 Visualizing the Performance of Scoring Classifiers
ROI-1.0-0 R Optimization Infrastructure
ROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’
RPMM-1.25 Recursively Partitioned Mixture Model
RPostgreSQL-0.7-3 R Interface to the ‘PostgreSQL’ Database System
RPresto-1.3.7 DBI Connector to Presto
RProtoBuf-0.4.17 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)
RProtoBufLib-2.6.0 C++ headers and static libraries of Protocol buffers
RSNNS-0.4-14 Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
RSQLite-2.2.8 ‘SQLite’ Interface for R
RSclient-0.7-6 Client for Rserve
RSpectra-0.16-0 Solvers for Large-Scale Eigenvalue and SVD Problems
RUnit-0.4.32 R Unit Test Framework
RWeka-0.4-43 R/Weka Interface
RWekajars-3.9.3-2 R/Weka Interface Jars
Rborist-0.2-3 Extensible, Parallelizable Implementation of the Random Forest Algorithm
Rcgmin-2013-2.21 Conjugate Gradient Minimization of Nonlinear Functions
Rcpp-1.0.7 Seamless R and C++ Integration
RcppAnnoy-0.0.19 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest Neighbors
RcppArmadillo-0.10.7.0.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library
RcppCCTZ-0.2.9 ‘Rcpp’ Bindings for the ‘CCTZ’ Library
RcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time Functionality
RcppEigen-0.3.3.9.1 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra Library
RcppGSL-0.3.10 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and Matrices
RcppHNSW-0.3.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest Neighbors
RcppNumerical-0.4-0 ‘Rcpp’ Integration for Numerical Computing Libraries
RcppParallel-5.1.4 Parallel Programming Tools for ‘Rcpp’
RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R Packages
RcppRoll-0.3.0 Efficient Rolling / Windowed Operations
RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG Implementations
Rdpack-2.1.2 Update and Manipulate Rd Documentation Objects
Rdsdp-1.0.5.1 R Interface to DSDP Semidefinite Programming Library
RefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture Deconvolution
ReportingTools-2.34.0 Tools for making reports in various formats
Rfast-2.0.3 A Collection of Efficient and Extremely Fast R Functions
Rglpk-0.6-4 R/GNU Linear Programming Kit Interface
Rgraphviz-2.38.0 Provides plotting capabilities for R graph objects
Rhdf5lib-1.16.0 hdf5 library as an R package
Rhpc-0.21-247 Permits apply() Style Dispatch for ‘HPC’
Rhtslib-1.26.0 HTSlib high-throughput sequencing library as an R package
Ringo-1.58.0 R Investigation of ChIP-chip Oligoarrays
Rlabkey-2.8.1 Data Exchange Between R and ‘LabKey’ Server
Rmpi-0.6-9.2 Interface (Wrapper) to MPI (Message-Passing Interface)
Rook-1.1-1 Rook - a web server interface for R
Rsamtools-2.10.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Rserve-1.7-3.1 Binary R server
Rsolnp-1.16 General Non-Linear Optimization
Rssa-1.0.4 A Collection of Methods for Singular Spectrum Analysis
Rsubread-2.8.1 Mapping, quantification and variant analysis of sequencing data
Rtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
Rttf2pt1-1.3.9 ‘ttf2pt1’ Program
Rvmmin-2018-4.17.1 Variable Metric Nonlinear Function Minimization
S4Vectors-0.32.3 Foundation of vector-like and list-like containers in Bioconductor
SBdecomp-1.1 Estimation of the Proportion of SB Explained by Confounders
SDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
SKAT-2.0.1 SNP-Set (Sequence) Kernel Association Test
SNPRelate-1.28.0 Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)
SNPassoc-2.0-2 SNPs-Based Whole Genome Association Studies
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-2.46.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
SQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
ScaledMatrix-1.2.0 Creating a DelayedMatrix of Scaled and Centered Values
SemiPar-1.0-4.2 Semiparametic Regression
SeqArray-1.34.0 Data management of large-scale whole-genome sequence variant calls
SeqVarTools-1.32.0 Tools for variant data
ShortRead-1.52.0 FASTQ input and manipulation
SignifReg-4.2 Consistent Significance Controlled Variable Selection in Generalized Linear Regression
SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
SingleCellExperiment-1.16.0 S4 Classes for Single Cell Data
SnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 Library
SparseM-1.81 Sparse Linear Algebra
StanHeaders-2.21.0-7 C++ Header Files for Stan
SummarizedExperiment-1.24.0 SummarizedExperiment container
SuperLearner-2.0-28 Super Learner Prediction
SuppDists-1.1-9.5 Supplementary Distributions
TFBSTools-1.32.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
TFMPvalue-0.0.8 Efficient and Accurate P-Value Computation for Position Weight Matrices
TFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination Method
TH.data-1.1-0 TH’s Data Archive
TMB-1.7.22 Template Model Builder: A General Random Effect Tool Inspired by ‘ADMB’
TTR-0.24.2 Technical Trading Rules
TeachingDemos-2.12 Demonstrations for Teaching and Learning
TitanCNA-1.32.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
TraMineR-2.2-2 Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)
UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
V8-3.4.2 Embedded JavaScript and WebAssembly Engine for R
VGAM-1.1-5 Vector Generalized Linear and Additive Models
VIM-6.1.1 Visualization and Imputation of Missing Values
VSURF-1.1.0 Variable Selection Using Random Forests
VariantAnnotation-1.40.0 Annotation of Genetic Variants
VennDiagram-1.7.0 Generate High-Resolution Venn and Euler Plots
WeightSVM-1.7-9 Subject Weighted Support Vector Machines
WikidataQueryServiceR-1.0.0 API Client Library for ‘Wikidata Query Service’
WikidataR-2.3.1 Read-Write API Client Library for Wikidata
WikipediR-1.5.0 A MediaWiki API Wrapper
Wrench-1.12.0 Wrench normalization for sparse count data
WriteXLS-6.3.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files
XML-3.99-0.8 Tools for Parsing and Generating XML Within R and S-Plus
XVector-0.34.0 Foundation of external vector representation and manipulation in Bioconductor
abc-2.1 Tools for Approximate Bayesian Computation (ABC)
abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)
abe-3.0.1 Augmented Backward Elimination
abind-1.4-5 Combine Multidimensional Arrays
acepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformations
adabag-4.2 Applies Multiclass AdaBoost.M1, SAMME and Bagging
ade4-1.7-18 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
admisc-0.20 Adrian Dusa’s Miscellaneous
affxparser-1.66.0 Affymetrix File Parsing SDK
affy-1.72.0 Methods for Affymetrix Oligonucleotide Arrays
affycoretools-1.66.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
affyio-1.64.0 Tools for parsing Affymetrix data files
aggregation-1.0.1 p-Value Aggregation Methods
akima-0.6-2.2 Interpolation of Irregularly and Regularly Spaced Data
alabama-2015.3-1 Constrained Nonlinear Optimization
alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
amap-0.8-18 Another Multidimensional Analysis Package
animation-2.7 A Gallery of Animations in Statistics and Utilities to Create Animations
annaffy-1.66.0 Annotation tools for Affymetrix biological metadata
annotate-1.72.0 Annotation for microarrays
aod-1.3.1 Analysis of Overdispersed Data
ape-5.5 Analyses of Phylogenetics and Evolution
apeglm-1.16.0 Approximate posterior estimation for GLM coefficients
aplot-0.1.1 Decorate a ‘ggplot’ with Associated Information
argparse-2.1.2 Command Line Optional and Positional Argument Parser
argparser-0.7.1 Command-Line Argument Parser
arm-1.12-2 Data Analysis Using Regression and Multilevel/Hierarchical Models
arsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical Summaries
arules-1.7-1 Mining Association Rules and Frequent Itemsets
ash-1.0-15 David Scott’s ASH Routines
ashr-2.2-47 Methods for Adaptive Shrinkage, using Empirical Bayes
askpass-1.1 Safe Password Entry for R, Git, and SSH
asnipe-1.1.16 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-0.0-3 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-0.0-4 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
audio-0.1-8 Audio Interface for R
aws-2.5-1 Adaptive Weights Smoothing
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
awsMethods-1.1-1 Class and Methods Definitions for Packages ‘aws’, ‘adimpro’, ‘fmri’, ‘dwi’
babelgene-21.4 Gene Orthologs for Model Organisms in a Tidy Data Format
backports-1.3.0 Reimplementations of Functions Introduced Since R-3.0.0
bacr-1.0.1 Bayesian Adjustment for Confounding
bamsignals-1.26.0 Extract read count signals from bam files
bartMachine-1.2.6 Bayesian Additive Regression Trees
bartMachineJARs-1.1 bartMachine JARs
base built in
base64-2.0 Base64 Encoder and Decoder
base64enc-0.1-3 Tools for base64 encoding
base64url-1.4 Fast and URL-Safe Base64 Encoder and Decoder
batchmeans-1.0-4 Consistent Batch Means Estimation of Monte Carlo Standard Errors
batchtools-0.9.15 Tools for Computation on Batch Systems
baySeq-2.28.0 Empirical Bayesian analysis of patterns of differential expression in count data
bayesm-3.1-4 Bayesian Inference for Marketing/Micro-Econometrics
bayesplot-1.8.1 Plotting for Bayesian Models
bbmle-1.0.24 Tools for General Maximum Likelihood Estimation
bdsmatrix-1.3-4 Routines for Block Diagonal Symmetric Matrices
beachmat-2.10.0 Compiling Bioconductor to Handle Each Matrix Type
beanplot-1.2 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
betareg-3.1-4 Beta Regression
bezier-1.1.2 Toolkit for Bezier Curves and Splines
bibtex-0.4.2.3 Bibtex Parser
biglm-0.9-2.1 Bounded Memory Linear and Generalized Linear Models
bigmemory-4.5.36 Manage Massive Matrices with Shared Memory and Memory-Mapped Files
bigmemory.sri-0.1.3 A shared resource interface for Bigmemory Project packages
bindr-0.1.1 Parametrized Active Bindings
bindrcpp-0.2.2 An ‘Rcpp’ Interface to Active Bindings
bio3d-2.4-2 Biological Structure Analysis
biom-0.3.12 An interface package (beta) for the BIOM file format.
biomaRt-2.50.1 Interface to BioMart databases (i.e. Ensembl)
biomformat-1.22.0 An interface package for the BIOM file format
biomod2-3.5.1 Ensemble Platform for Species Distribution Modeling
biovizBase-1.42.0 Basic graphic utilities for visualization of genomic data.
bit-4.0.4 Classes and Methods for Fast Memory-Efficient Boolean Selections
bit64-4.0.5 A S3 Class for Vectors of 64bit Integers
bitops-1.0-7 Bitwise Operations
blavaan-0.3-17 Bayesian Latent Variable Analysis
blob-1.2.2 A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’)
bmp-0.3 Read Windows Bitmap (BMP) Images
bnlearn-4.7 Bayesian Network Structure Learning, Parameter Learning and Inference
bold-1.2.0 Interface to Bold Systems API
bookdown-0.24 Authoring Books and Technical Documents with R Markdown
boot-1.3-28 Bootstrap Functions (Originally by Angelo Canty for S)
bootstrap-2019.6 Functions for the Book “An Introduction to the Bootstrap”
breakaway-3.0 Species Richness Estimation and Modeling
brew-1.0-6 Templating Framework for Report Generation
brglm-0.7.2 Bias Reduction in Binomial-Response Generalized Linear Models
bridgedist-0.1.0 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-1.1.2 Basic R Input Output
brms-2.16.1 Bayesian Regression Models using ‘Stan’
broom-0.7.10 Convert Statistical Objects into Tidy Tibbles
broom.helpers-1.4.0 Helpers for Model Coefficients Tibbles
broom.mixed-0.2.7 Tidying Methods for Mixed Models
bslib-0.3.1 Custom ‘Bootstrap’ ‘Sass’ Themes for ‘shiny’ and ‘rmarkdown’
bst-0.3-23 Gradient Boosting
bumphunter-1.36.0 Bump Hunter
cNORM-2.1.0 Continuous Norming
cSEM-0.4.0 Composite-Based Structural Equation Modeling
caTools-1.18.2 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
cachem-1.0.6 Cache R Objects with Automatic Pruning
calibrate-1.7.7 Calibration of Scatterplot and Biplot Axes
callr-3.7.0 Call R from R
car-3.0-11 Companion to Applied Regression
carData-3.0-4 Companion to Applied Regression Data Sets
caret-6.0-90 Classification and Regression Training
catdata-1.2.2 Categorical Data
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 regression.
checkmate-2.0.0 Fast and Versatile Argument Checks
chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
chipseq-1.44.0 chipseq: A package for analyzing chipseq data
chromVAR-1.16.0 Chromatin Variation Across Regions
chron-2.3-56 Chronological Objects which can Handle Dates and Times
circlize-0.4.13 Circular Visualization
circular-0.4-93 Circular Statistics
clValid-0.7 Validation of Clustering Results
class-7.3-19 Functions for Classification
classInt-0.4-3 Choose Univariate Class Intervals
cli-3.1.0 Helpers for Developing Command Line Interfaces
clipr-0.7.1 Read and Write from the System Clipboard
clisymbols-1.2.0 Unicode Symbols at the R Prompt
clue-0.3-60 Cluster Ensembles
cluster-2.1.2 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al.
clusterGeneration-1.3.7 Random Cluster Generation (with Specified Degree of Separation)
clusterProfiler-4.2.0 A universal enrichment tool for interpreting omics data
clusterRepro-0.9 Reproducibility of Gene Expression Clusters
clustree-0.4.3 Visualise Clusterings at Different Resolutions
cobalt-4.3.1 Covariate Balance Tables and Plots
cobs-1.3-4 Constrained B-Splines (Sparse Matrix Based)
coda-0.19-4 Output Analysis and Diagnostics for MCMC
codetools-0.2-18 Code Analysis Tools for R
coin-1.4-2 Conditional Inference Procedures in a Permutation Test Framework
colorRamps-2.3 Builds color tables
colorspace-2.0-2 A Toolbox for Manipulating and Assessing Colors and Palettes
colourpicker-1.1.1 A Colour Picker Tool for Shiny and for Selecting Colours in Plots
combinat-0.0-8 combinatorics utilities
commonmark-1.7 High Performance CommonMark and Github Markdown Rendering in R
compare-0.2-6 Comparing Objects for Differences
compiler built in
compositions-2.0-2 Compositional Data Analysis
conditionz-0.1.0 Control How Many Times Conditions are Thrown
config-0.3.1 Manage Environment Specific Configuration Values
conflicted-1.0.4 An Alternative Conflict Resolution Strategy
conquer-1.2.0 Convolution-Type Smoothed Quantile Regression
copCAR-2.0-4 Fitting the copCAR Regression Model for Discrete Areal Data
copula-1.0-1 Multivariate Dependence with Copulas
copynumber-1.34.0 Segmentation of single- and multi-track copy number data by penalized least squares regression.
corpcor-1.6.10 Efficient Estimation of Covariance and (Partial) Correlation
corrplot-0.90 Visualization of a Correlation Matrix
covr-3.5.1 Test Coverage for Packages
cowplot-1.1.1 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
coxed-0.3.3 Duration-Based Quantities of Interest for the Cox Proportional Hazards Model
coxme-2.2-16 Mixed Effects Cox Models
cpp11-0.4.0 A C++11 Interface for R’s C Interface
crayon-1.4.2 Colored Terminal Output
credentials-1.3.1 Tools for Managing SSH and Git Credentials
crosstalk-1.1.1 Inter-Widget Interactivity for HTML Widgets
crul-1.1.0 HTTP Client
csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
ctmle-0.1.2 Collaborative Targeted Maximum Likelihood Estimation
cubature-2.0.4.2 Adaptive Multivariate Integration over Hypercubes
cubelyr-1.0.1 A Data Cube ‘dplyr’ Backend
cummeRbund-2.36.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
curl-4.3.2 A Modern and Flexible Web Client for R
curry-0.1.1 Partial Function Application with %<%, %-<%, and %><%
cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
cyclocomp-1.1.0 Cyclomatic Complexity of R Code
cytolib-2.6.0 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 Sankey graphs from R
dHSIC-2.1 Independence Testing via Hilbert Schmidt Independence Criterion
dada2-1.22.0 Accurate, high-resolution sample inference from amplicon sequencing data
data.table-1.14.2 Extension of data.frame
data.tree-1.0.0 General Purpose Hierarchical Data Structure
datasets built in
dbarts-0.9-20 Discrete Bayesian Additive Regression Trees Sampler
dbplyr-2.1.1 A ‘dplyr’ Back End for Databases
dbscan-1.1-8 Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms
ddalpha-1.3.11 Depth-Based Classification and Calculation of Data Depth
deSolve-1.30 Solvers for Initial Value Problems of Differential Equations (‘ODE’, ‘DAE’, ‘DDE’)
deal-1.2-39 Learning Bayesian Networks with Mixed Variables
debugme-1.1.0 Debug R Packages
degreenet-1.3-3 Models for Skewed Count Distributions Relevant to Networks
deldir-1.0-6 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
dendextend-1.15.2 Extending ‘dendrogram’ Functionality in R
derfinder-1.28.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
derfinderHelper-1.28.0 derfinder helper package
desc-1.4.0 Manipulate DESCRIPTION Files
descr-1.1.5 Descriptive Statistics
devtools-2.4.2 Tools to Make Developing R Packages Easier
dfidx-0.0-4 Indexed Data Frames
dfoptim-2020.10-1 Derivative-Free Optimization
diagram-1.6.5 Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
dials-0.0.10 Tools for Creating Tuning Parameter Values
diamonds-1.0-5 Analysis and sampling grids from diamond partitions
dichromat-2.0-0 Color Schemes for Dichromats
diffobj-0.3.5 Diffs for R Objects
diffusionMap-1.2.0 Diffusion Map
digest-0.6.28 Create Compact Hash Digests of R Objects
dimRed-0.2.3 A Framework for Dimensionality Reduction
diptest-0.76-0 Hartigan’s Dip Test Statistic for Unimodality - Corrected
dismo-1.3-5 Species Distribution Modeling
distillery-1.2-1 Method Functions for Confidence Intervals and to Distill Information from an Object
distr-2.8.0 Object Oriented Implementation of Distributions
distrEx-2.8.0 Extensions of Package ‘distr’
distributional-0.2.2 Vectorised Probability Distributions
diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis Package
doBy-4.6.11 Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
doMC-1.3.7 Foreach Parallel Adaptor for ‘parallel’
doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
doParallel-1.0.16 Foreach Parallel Adaptor for the ‘parallel’ Package
doRNG-1.8.2 Generic Reproducible Parallel Backend for ‘foreach’ Loops
doSNOW-1.0.19 Foreach Parallel Adaptor for the ‘snow’ Package
dotCall64-1.0-1 Enhanced Foreign Function Interface Supporting Long Vectors
downloader-0.4 Download Files over HTTP and HTTPS
dplyr-1.0.7 A Grammar of Data Manipulation
dqrng-0.3.0 Fast Pseudo Random Number Generators
dr-3.0.10 Methods for Dimension Reduction for Regression
drc-3.0-1 Analysis of Dose-Response Curves
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-1.1.0 Data Table Back-End for ‘dplyr’
dtw-1.22-3 Dynamic Time Warping Algorithms
dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
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
e1071-1.7-9 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
earth-5.3.1 Multivariate Adaptive Regression Splines
edgeR-3.36.0 Empirical Analysis of Digital Gene Expression Data in R
elasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCA
elementR-1.3.7 An Framework for Reducing Elemental LAICPMS Data from Solid Structures
ellipse-0.4.2 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
ellipsis-0.3.2 Tools for Working with …
emdbook-1.3.12 Support Functions and Data for “Ecological Models and Data”
emulator-1.2-21 Bayesian Emulation of Computer Programs
energy-1.7-8 E-Statistics: Multivariate Inference via the Energy of Data
enrichplot-1.14.1 Visualization of Functional Enrichment Result
ensembldb-2.18.2 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-4.1.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks
ergm.count-4.0.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
etrunct-0.1 Computes Moments of Univariate Truncated t Distribution
europepmc-0.4.1 R Interface to the Europe PubMed Central RESTful Web Service
evaluate-0.14 Parsing and Evaluation Tools that Provide More Details than the Default
expm-0.999-6 Matrix Exponential, Log, ‘etc’
expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
extRemes-2.1-1 Extreme Value Analysis
extrafont-0.17 Tools for using fonts
extrafontdb-1.0 Package for holding the database for the extrafont package
fANCOVA-0.6-1 Nonparametric Analysis of Covariance
fail-1.3 File Abstraction Interface Layer (FAIL)
fansi-0.5.0 ANSI Control Sequence Aware String Functions
faraway-1.0.7 Functions and Datasets for Books by Julian Faraway
farver-2.1.0 High Performance Colour Space Manipulation
fastICA-1.2-3 FastICA Algorithms to Perform ICA and Projection Pursuit
fastcluster-1.2.3 Fast Hierarchical Clustering Routines for R and ‘Python’
fasterize-1.0.3 Fast Polygon to Raster Conversion
fastmap-1.1.0 Fast Data Structures
fastmatch-1.1-3 Fast ‘match()’ Function
fastseg-1.40.0 fastseg - a fast segmentation algorithm
fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
fda-5.5.1 Functional Data Analysis
fdrtool-1.2.16 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’
ff-4.0.5 Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
ffbase-0.13.3 Basic Statistical Functions for Package ‘ff’
fftw-1.0-6 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-1.20.0 Fast Gene Set Enrichment Analysis
fields-13.3 Tools for Spatial Data
filehash-2.4-2 Simple Key-Value Database
filelock-1.0.2 Portable File Locking
finalfit-1.0.3 Quickly Create Elegant Regression Results Tables and Plots when Modelling
findpython-1.0.7 Functions to Find an Acceptable Python Binary
fishMod-0.29 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta Log-Normal Models
fit.models-0.64 Compare Fitted Models
fitdistrplus-1.1-6 Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
flashClust-1.01-2 Implementation of optimal hierarchical clustering
flexclust-1.4-0 Flexible Cluster Algorithms
flexmix-2.3-17 Flexible Mixture Modeling
flowClust-3.32.0 Clustering for Flow Cytometry
flowCore-2.6.0 flowCore: Basic structures for flow cytometry data
flowStats-4.6.0 Statistical methods for the analysis of flow cytometry data
flowViz-1.58.0 Visualization for flow cytometry
flowWorkspace-4.6.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
fma-2.4 Data Sets from “Forecasting: Methods and Applications” by Makridakis, Wheelwright & Hyndman (1998)
fmri-1.9.6 Analysis of fMRI Experiments
fontawesome-0.2.2 Easily Work with ‘Font Awesome’ Icons
forcats-0.5.1 Tools for Working with Categorical Variables (Factors)
foreach-1.5.1 Provides Foreach Looping Construct
forecast-8.15 Forecasting Functions for Time Series and Linear Models
foreign-0.8-81 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …
forestplot-2.0.1 Advanced Forest Plot Using ‘grid’ Graphics
forge-0.2.0 Casting Values into Shape
formatR-1.11 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-2.2-9 Flexible Procedures for Clustering
fpp-0.5 Data for “Forecasting: principles and practice”
fracdiff-1.5-1 Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
fs-1.5.0 Cross-Platform File System Operations Based on ‘libuv’
fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
furrr-0.2.3 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-1.23.0 Unified Parallel and Distributed Processing in R for Everyone
future.apply-1.8.1 Apply Function to Elements in Parallel using Futures
gWidgets2-1.0-8 Rewrite of gWidgets API for Simplified GUI Construction
gWidgets2tcltk-1.0-6 Toolkit Implementation of gWidgets2 for tcltk
gage-2.44.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
gam-1.20 Generalized Additive Models
gamlss-5.3-4 Generalised Additive Models for Location Scale and Shape
gamlss.data-6.0-1 Data for Generalised Additive Models for Location Scale and Shape
gamlss.dist-5.3-2 Distributions for Generalized Additive Models for Location Scale and Shape
gamlss.tr-5.1-7 Generating and Fitting Truncated `gamlss.family’ Distributions
gamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
gap-1.2.3-1 Genetic Analysis Package
gapfill-0.9.6-1 Fill Missing Values in Satellite Data
gargle-1.2.0 Utilities for Working with Google APIs
gaussquad-1.0-2 Collection of functions for Gaussian quadrature
gbRd-0.4-11 Utilities for processing Rd objects and files
gbm-2.1.8 Generalized Boosted Regression Models
gclus-1.3.2 Clustering Graphics
gcrma-2.66.0 Background Adjustment Using Sequence Information
gdata-2.18.0 Various R Programming Tools for Data Manipulation
gdistance-1.3-6 Distances and Routes on Geographical Grids
gdsfmt-1.30.0 R Interface to CoreArray Genomic Data Structure (GDS) files
gdtools-0.2.3 Utilities for Graphical Rendering
gee-4.13-20 Generalized Estimation Equation Solver
geepack-1.3-2 Generalized Estimating Equation Package
geiger-2.0.7 Analysis of Evolutionary Diversification
geneLenDataBase-1.30.0 Lengths of mRNA transcripts for a number of genomes
genefilter-1.76.0 genefilter: methods for filtering genes from high-throughput experiments
geneplotter-1.72.0 Graphics related functions for Bioconductor
generics-0.1.1 Common S3 Generics not Provided by Base R Methods Related to Model Fitting
geometry-0.4.5 Mesh Generation and Surface Tessellation
gert-1.4.1 Simple Git Client for R
getopt-1.20.3 C-Like ‘getopt’ Behavior
ggExtra-0.9 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’ Enhancements
ggbeeswarm-0.6.0 Categorical Scatter (Violin Point) Plots
ggbio-1.42.0 Visualization tools for genomic data
ggcyto-1.22.0 Visualize Cytometry data with ggplot
ggdendro-0.1.22 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
ggfan-0.1.3 Summarise a Distribution Through Coloured Intervals
ggforce-0.3.3 Accelerating ‘ggplot2’
ggfun-0.0.4 Miscellaneous Functions for ‘ggplot2’
ggnetwork-0.5.10 Geometries to Plot Networks with ‘ggplot2’
ggnewscale-0.4.5 Multiple Fill and Colour Scales in ‘ggplot2’
ggplot2-3.3.5 Create Elegant Data Visualisations Using the Grammar of Graphics
ggplotify-0.1.0 Convert Plot to ‘grob’ or ‘ggplot’ Object
ggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plot
ggpubr-0.4.0 ‘ggplot2’ Based Publication Ready Plots
ggraph-2.0.5 An Implementation of Grammar of Graphics for Graphs and Networks
ggrepel-0.9.1 Automatically Position Non-Overlapping Text Labels with ‘ggplot2’
ggridges-0.5.3 Ridgeline Plots in ‘ggplot2’
ggsci-2.9 Scientific Journal and Sci-Fi Themed Color Palettes for ‘ggplot2’
ggsignif-0.6.3 Significance Brackets for ‘ggplot2’
ggthemes-4.2.4 Extra Themes, Scales and Geoms for ‘ggplot2’
ggtree-3.2.1 an R package for visualization of tree and annotation data
ggvis-0.4.7 Interactive Grammar of Graphics
gh-1.3.0 ‘GitHub’ ‘API’
git2r-0.28.0 Provides Access to Git Repositories
gitcreds-0.1.1 Query ‘git’ Credentials from ‘R’
glasso-1.11 Graphical Lasso: Estimation of Gaussian Graphical Models
gld-2.6.2 Estimation and Use of the Generalised (Tukey) Lambda Distribution
gllvm-1.3.1 Generalized Linear Latent Variable Models
glmmML-1.1.1 Generalized Linear Models with Clustering
glmmTMB-1.1.2.3 Generalized Linear Mixed Models using Template Model Builder
glmnet-4.1-2 Lasso and Elastic-Net Regularized Generalized Linear Models
glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model
globals-0.14.0 Identify Global Objects in R Expressions
glue-1.4.2 Interpreted String Literals
gmm-1.6-6 Generalized Method of Moments and Generalized Empirical Likelihood
gmodels-2.18.1 Various R Programming Tools for Model Fitting
gmp-0.6-2 Multiple Precision Arithmetic
gnumeric-0.7-8 Read Data from Files Readable by ‘gnumeric’
goftest-1.2-3 Classical Goodness-of-Fit Tests for Univariate Distributions
gomms-1.0 GLM-Based Ordination Method
googledrive-2.0.0 An Interface to Google Drive
googlesheets4-1.0.0 Access Google Sheets using the Sheets API V4
goseq-1.46.0 Gene Ontology analyser for RNA-seq and other length biased data
gower-0.2.2 Gower’s Distance
gplots-3.1.1 Various R Programming Tools for Plotting Data
grDevices built in
grImport2-0.2-0 Importing ‘SVG’ Graphics
graph-1.72.0 graph: A package to handle graph data structures
graphics built in
graphlayouts-0.7.1 Additional Layout Algorithms for Network Visualizations
grf-2.0.2 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-3.4.0 Regularization Paths for Regression Models with Grouped Covariates
gsalib-2.1 Utility Functions For GATK
gsl-2.1-7 Wrapper for the Gnu Scientific Library
gsubfn-0.7 Utilities for Strings and Function Arguments
gsw-1.0-6 Gibbs Sea Water Functions
gt-0.3.1 Easily Create Presentation-Ready Display Tables
gtable-0.3.0 Arrange ‘Grobs’ in Tables
gtools-3.9.2 Various R Programming Tools
gtsummary-1.5.0 Presentation-Ready Data Summary and Analytic Result Tables
h2o-3.34.0.3 R Interface for the ‘H2O’ Scalable Machine Learning Platform
hal9001-0.4.1 The Scalable Highly Adaptive Lasso
hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
haplo.stats-1.8.7 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
hardhat-0.1.6 Construct Modeling Packages
haven-2.4.3 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
hdf5r-1.3.4 Interface to the ‘HDF5’ Binary Data Format
hdm-0.3.1 High-Dimensional Metrics
hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
heatmap3-1.1.9 An Improved Heatmap Package
here-1.0.1 A Simpler Way to Find Your Files
hexbin-1.28.2 Hexagonal Binning Routines
hgu133plus2.db-3.13.0 Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)
highr-0.9 Syntax Highlighting for R Source Code
hms-1.1.1 Pretty Time of Day
hopach-2.54.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
htmlTable-2.3.0 Advanced Tables for Markdown/HTML
htmltools-0.5.2 Tools for HTML
htmlwidgets-1.5.4 HTML Widgets for R
httpcode-0.3.0 ‘HTTP’ Status Code Helper
httpuv-1.6.3 HTTP and WebSocket Server Library
httr-1.4.2 Tools for Working with URLs and HTTP
huge-1.3.5 High-Dimensional Undirected Graph Estimation
hunspell-3.0.1 High-Performance Stemmer, Tokenizer, and Spell Checker
hwriter-1.3.2 HTML Writer - Outputs R objects in HTML format
hypergate-0.8.3 Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry
ica-1.0-2 Independent Component Analysis
idr-1.2 Irreproducible discovery rate
ids-1.0.1 Generate Random Identifiers
ie2misc-0.8.6 Irucka Embry’s Miscellaneous USGS Functions
igraph-1.2.7 Network Analysis and Visualization
igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
illuminaio-0.36.0 Parsing Illumina Microarray Output Files
image.binarization-0.1.2 Binarize Images for Enhancing Optical Character Recognition
imager-0.42.10 Image Processing Library Based on ‘CImg’
imagerExtra-1.3.2 Extra Image Processing Library Based on ‘imager’
impute-1.68.0 impute: Imputation for microarray data
ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
infer-1.0.0 Tidy Statistical Inference
inferference-1.0.2 Methods for Causal Inference with Interference
influenceR-0.1.0.1 Software Tools to Quantify Structural Importance of Nodes in a Network
infotheo-1.2.0 Information-Theoretic Measures
ini-0.3.1 Read and Write ‘.ini’ Files
inline-0.3.19 Functions to Inline C, C++, Fortran Function Calls from R
interactiveDisplayBase-1.32.0 Base package for enabling powerful shiny web displays of Bioconductor objects
intergraph-2.0-2 Coercion Routines for Network Data Objects
interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
intrinsicDimension-1.2.0 Intrinsic Dimension Estimation
inum-1.0-4 Interval and Enum-Type Representation of Vectors
invgamma-1.1 The Inverse Gamma Distribution
iotools-0.3-2 I/O Tools for Streaming
ipred-0.9-12 Improved Predictors
irace-3.4.1 Iterated Racing for Automatic Algorithm Configuration
irlba-2.3.3 Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices
isoband-0.2.5 Generate Isolines and Isobands from Regularly Spaced Elevation Grids
iterators-1.0.13 Provides Iterator Construct
itertools-0.1-3 Iterator Tools
its-1.1.8 Irregular Time Series
janeaustenr-0.1.5 Jane Austen’s Complete Novels
jiebaR-0.11 Chinese Text Segmentation
jiebaRD-0.1 Chinese Text Segmentation Data for jiebaR Package
jomo-2.7-2 Multilevel Joint Modelling Multiple Imputation
jpeg-0.1-9 Read and write JPEG images
jquerylib-0.1.4 Obtain ‘jQuery’ as an HTML Dependency Object
jsonlite-1.7.2 A Simple and Robust JSON Parser and Generator for R
jstable-1.0.7 Create Tables from Different Types of Regression
karyoploteR-1.20.0 Plot customizable linear genomes displaying arbitrary data
kedd-1.0.3 Kernel Estimator and Bandwidth Selection for Density and Its Derivatives
kernlab-0.9-29 Kernel-Based Machine Learning Lab
keyring-1.2.0 Access the System Credential Store from R
kin.cohort-0.7 Analysis of Kin-Cohort Studies
kinship2-1.8.5 Pedigree Functions
klaR-0.6-15 Classification and Visualization
knitr-1.36 A General-Purpose Package for Dynamic Report Generation in R
knockoff-0.3.3 The Knockoff Filter for Controlled Variable Selection
kohonen-3.0.10 Supervised and Unsupervised Self-Organising Maps
ks-1.13.2 Kernel Smoothing
kyotil-2021.5-14 Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
labdsv-2.0-1 Ordination and Multivariate Analysis for Ecology
labeling-0.4.2 Axis Labeling
labelled-2.9.0 Manipulating Labelled Data
laeken-0.5.2 Estimation of Indicators on Social Exclusion and Poverty
lambda.r-1.2.4 Modeling Data with Functional Programming
lars-1.2 Least Angle Regression, Lasso and Forward Stagewise
lasso2-1.2-22 L1 Constrained Estimation aka `lasso’
lassosum 0.4.5
latentnet-2.10.5 Latent Position and Cluster Models for Statistical Networks
later-1.3.0 Utilities for Scheduling Functions to Execute Later with Event Loops
lattice-0.20-45 Trellis Graphics for R
latticeExtra-0.6-29 Extra Graphical Utilities Based on Lattice
lava-1.6.10 Latent Variable Models
lavaan-0.6-9 Latent Variable Analysis
lazy-1.2-16 Lazy Learning for Local Regression
lazyeval-0.2.2 Lazy (Non-Standard) Evaluation
lda-1.4.2 Collapsed Gibbs Sampling Methods for Topic Models
leaps-3.1 Regression Subset Selection
leiden-0.3.9 R Implementation of Leiden Clustering Algorithm
lhs-1.1.3 Latin Hypercube Samples
libcoin-1.0-9 Linear Test Statistics for Permutation Inference
lifecycle-1.0.1 Manage the Life Cycle of your Package Functions
limSolve-1.5.6 Solving Linear Inverse Models
limma-3.50.0 Linear Models for Microarray Data
linkcomm-1.0-14 Tools for Generating, Visualizing, and Analysing Link Communities in Networks
linprog-0.9-2 Linear Programming / Optimization
lintr-2.0.1 A ‘Linter’ for R Code
liquidSVM-1.2.4 A Fast and Versatile SVM Package
listenv-0.8.0 Environments Behaving (Almost) as Lists
lme4-1.1-27.1 Linear Mixed-Effects Models using ‘Eigen’ and S4
lmerTest-3.1-3 Tests in Linear Mixed Effects Models
lmom-2.8 L-Moments
lmtest-0.9-38 Testing Linear Regression Models
lobstr-1.1.1 Visualize R Data Structures with Trees
locfdr-1.1-8 Computes Local False Discovery Rates
locfit-1.5-9.4 Local Regression, Likelihood and Density Estimation
logcondens-2.1.6 Estimate a Log-Concave Probability Density from Iid Observations
logistf-1.24 Firth’s Bias-Reduced Logistic Regression
logspline-2.1.16 Routines for Logspline Density Estimation
lokern-1.1-9 Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
longitudinal-1.1.12 Analysis of Multiple Time Course Data
longmemo-1.1-2 Statistics for Long-Memory Processes (Book Jan Beran), and Related Functionality
loo-2.4.1 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
lpSolve-5.6.15 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
lpSolveAPI-5.5.2.0-17.7 R Interface to ‘lp_solve’ Version 5.5.2.0
lpridge-1.0-8 Local Polynomial (Ridge) Regression
lpsymphony-1.22.0 Symphony integer linear programming solver in R
lqa-1.0-3 Penalized Likelihood Inference for GLMs
lsei-1.3-0 Solving Least Squares or Quadratic Programming Problems under Equality/Inequality Constraints
lslx-0.6.10 Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood or Least Squares
lubridate-1.8.0 Make Dealing with Dates a Little Easier
lumi-2.46.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
lwgeom-0.2-8 Bindings to Selected ‘liblwgeom’ Functions for Simple Features
mRMRe-2.1.2 Parallelized Minimum Redundancy, Maximum Relevance (mRMR)
maSigPro-1.66.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
magic-1.5-9 Create and Investigate Magic Squares
magick-2.7.3 Advanced Graphics and Image-Processing in R
magrittr-2.0.1 A Forward-Pipe Operator for R
manipulateWidget-0.11.1 Add Even More Interactivity to Interactive Charts
mapdata-2.3.0 Extra Map Databases
mapproj-1.2.7 Map Projections
maps-3.4.0 Draw Geographical Maps
maptools-1.1-2 Tools for Handling Spatial Objects
markdown-1.1 Render Markdown with the C Library ‘Sundown’
marray-1.72.0 Exploratory analysis for two-color spotted microarray data
mathjaxr-1.4-0 Using ‘Mathjax’ in Rd Files
matrixStats-0.61.0 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
matrixcalc-1.0-5 Collection of Functions for Matrix Calculations
maxLik-1.5-2 Maximum Likelihood Estimation and Related Tools
maxlike-0.1-8 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-2.9-5 Model-Based Boosting
mclust-5.4.7 Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
mcmc-0.9-7 Markov Chain Monte Carlo
mcmcse-1.5-0 Monte Carlo Standard Errors for MCMC
mda-0.5-2 Mixture and Flexible Discriminant Analysis
medflex-0.6-7 Flexible Mediation Analysis Using Natural Effect Models
mediation-4.5.0 Causal Mediation Analysis
memoise-2.0.0 ‘Memoisation’ of Functions
memuse-4.2-1 Memory Estimation Utilities
metafor-3.0-2 Meta-Analysis Package for R
metagenomeSeq-1.36.0 Statistical analysis for sparse high-throughput sequencing
methods built in
methylKit-1.20.0 DNA methylation analysis from high-throughput bisulfite sequencing results
methylumi-2.40.1 Handle Illumina methylation data
mets-1.2.9 Analysis of Multivariate Event Times
mgcv-1.8-38 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
mgsub-1.7.3 Safe, Multiple, Simultaneous String Substitution
mhsmm-0.4.16 Inference for Hidden Markov and Semi-Markov Models
mi-1.0 Missing Data Imputation and Model Checking
mice-3.13.0 Multivariate Imputation by Chained Equations
miceadds-3.11-6 Some Additional Multiple Imputation Functions, Especially for ‘mice’
microbenchmark-1.4.9 Accurate Timing Functions
mime-0.12 Map Filenames to MIME Types
minerva-1.5.10 Maximal Information-Based Nonparametric Exploration for Variable Analysis
minfi-1.40.0 Analyze Illumina Infinium DNA methylation arrays
miniUI-0.1.1.1 Shiny UI Widgets for Small Screens
minpack.lm-1.2-1 R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds
minqa-1.2.4 Derivative-free optimization algorithms by quadratic approximation
misc3d-0.9-1 Miscellaneous 3D Plots
miscTools-0.6-26 Miscellaneous Tools and Utilities
missForest-1.4 Nonparametric Missing Value Imputation using Random Forest
mitml-0.4-3 Tools for Multiple Imputation in Multilevel Modeling
mitools-2.4 Tools for Multiple Imputation of Missing Data
mixOmics-6.18.1 Omics Data Integration Project
mixsqp-0.3-43 Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
mixtools-1.2.0 Tools for Analyzing Finite Mixture Models
mlbench-2.1-3 Machine Learning Benchmark Problems
mlegp-3.1.8 Maximum Likelihood Estimates of Gaussian Processes
mlogit-1.1-1 Multinomial Logit Models
mlr-2.19.0 Machine Learning in R
mltools-0.3.5 Machine Learning Tools
mnormt-2.0.2 The Multivariate Normal and t Distributions, and Their Truncated Versions
modeldata-0.1.1 Data Sets Used Useful for Modeling Packages
modelr-0.1.8 Modelling Functions that Work with the Pipe
modeltools-0.2-23 Tools and Classes for Statistical Models
moments-0.14 Moments, cumulants, skewness, kurtosis and related tests
mondate-0.10.02 Keep Track of Dates in Terms of Months
motifmatchr-1.16.0 Fast Motif Matching in R
mpath-0.4-2.19 Regularized Linear Models
msa-1.26.0 Multiple Sequence Alignment
msigdbr-7.4.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
msm-1.6.9 Multi-State Markov and Hidden Markov Models in Continuous Time
multcomp-1.4-17 Simultaneous Inference in General Parametric Models
multicool-0.1-12 Permutations of Multisets in Cool-Lex Order
multipol-1.0-7 Multivariate Polynomials
multtest-2.50.0 Resampling-based multiple hypothesis testing
munsell-0.5.0 Utilities for Using Munsell Colours
mvabund-4.1.12 Statistical Methods for Analysing Multivariate Abundance Data
mvnfast-0.2.7 Fast Multivariate Normal and Student’s t Methods
mvtnorm-1.1-3 Multivariate Normal and t Distributions
nabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low Dimensions
naniar-0.6.1 Data Structures, Summaries, and Visualisations for Missing Data
nanotime-0.3.4 Nanosecond-Resolution Time Support for R
natserv-1.0.0 ‘NatureServe’ Interface
naturalsort-0.1.3 Natural Ordering
ncbit-2013.03.29 retrieve and build NBCI taxonomic data
ncdf4-1.17 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
ncdfFlow-2.40.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
ndtv-0.13.2 Network Dynamic Temporal Visualizations
network-1.17.1 Classes for Relational Data
networkDynamic-0.11.0 Dynamic Extensions for Network Objects
networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
neuRosim-0.2-12 Functions to Generate fMRI Data Including Activated Data, Noise Data and Resting State 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-3.3.2 Solve Systems of Nonlinear Equations
nlme-3.1-153 Linear and Nonlinear Mixed Effects Models
nloptr-1.2.2.2 R Interface to NLopt
nlsem-0.8 Fitting Structural Equation Mixture Models
nnet-7.3-16 Feed-Forward Neural Networks and Multinomial Log-Linear Models
nnls-1.4 The Lawson-Hanson algorithm for non-negative least squares (NNLS)
nonnest2-0.5-5 Tests of Non-Nested Models
nor1mix-1.3-0 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods)
norm-1.0-9.5 Analysis of multivariate normal datasets with missing values
nortest-1.0-4 Tests for Normality
np-0.60-11 Nonparametric Kernel Smoothing Methods for Mixed Data Types
npsurv-0.5-0 Nonparametric Survival Analysis
numDeriv-2016.8-1.1 Accurate Numerical Derivatives
numbers-0.8-2 Number-Theoretic Functions
nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
oai-0.3.2 General Purpose ‘Oai-PMH’ Services Client
oce-1.4-0 Analysis of Oceanographic Data
odbc-1.3.2 Connect to ODBC Compatible Databases (using the DBI Interface)
oddsratio-2.0.1 Odds Ratio Calculation for GAM(M)s & GLM(M)s
oligo-1.58.0 Preprocessing tools for oligonucleotide arrays
oligoClasses-1.56.0 Classes for high-throughput arrays supported by oligo and crlmm
openCyto-2.6.0 Hierarchical Gating Pipeline for flow cytometry data
openssl-1.4.5 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
openxlsx-4.2.4 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
optimr-2019-12.16 A Replacement and Extension of the ‘optim’ Function
optimx-2021-10.12 Expanded Replacement and Extension of the ‘optim’ Function
optmatch-0.9-15 Functions for Optimal Matching
optparse-1.7.1 Command Line Option Parser
ordinal-2019.12-10 Regression Models for Ordinal Data
org.Hs.eg.db-3.14.0 Genome wide annotation for Human
org.Mm.eg.db-3.14.0 Genome wide annotation for Mouse
origami-1.0.5 Generalized Framework for Cross-Validation
oro.nifti-0.11.0 Rigorous - ‘NIfTI’ + ‘ANALYZE’ + ‘AFNI’ : Input / Output
orthopolynom-1.0-5 Collection of functions for orthogonal and orthonormal polynomials
outliers-0.14 Tests for outliers
pROC-1.18.0 Display and Analyze ROC Curves
pack-0.1-1 Convert values to/from raw vectors
packrat-0.7.0 A Dependency Management System for Projects and their R Package Dependencies
pacman-0.5.1 Package Management Tool
pamr-1.56.1 Pam: Prediction Analysis for Microarrays
pan-1.6 Multiple Imputation for Multivariate Panel or Clustered Data
parallel built in
parallelMap-1.5.1 Unified Interface to Parallelization Back-Ends
parallelly-1.28.1 Enhancing the ‘parallel’ Package
parsedate-1.2.1 Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats
parsnip-0.1.7 A Common API to Modeling and Analysis Functions
partools-1.1.6 Tools for the ‘Parallel’ Package
party-1.3-9 A Laboratory for Recursive Partytioning
partykit-1.2-15 A Toolkit for Recursive Partytioning
pastecs-1.3.21 Package for Analysis of Space-Time Ecological Series
patchwork-1.1.1 The Composer of Plots
pathview-1.34.0 a tool set for pathway based data integration and visualization
pbapply-1.5-0 Adding Progress Bar to ‘apply’ Functions
pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
pbkrtest-0.5.1 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models
pbs-1.1 Periodic B Splines
pcaMethods-1.86.0 A collection of PCA methods
pcaPP-1.9-74 Robust PCA by Projection Pursuit
pdftools-3.0.1 Text Extraction, Rendering and Converting of PDF Documents
pdist-1.2 Partitioned Distance Function
pedigree-1.4 Pedigree functions
pedigreemm-0.3-3 Pedigree-based mixed-effects models
penalized-0.9-51 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
peperr-1.3 Parallelised Estimation of Prediction Error
perm-1.0-0.2 Exact or Asymptotic Permutation Tests
permute-0.9-5 Functions for Generating Restricted Permutations of Data
phangorn-2.7.1 Phylogenetic Reconstruction and Analysis
pheatmap-1.0.12 Pretty Heatmaps
phylobase-0.8.10 Base Package for Phylogenetic Structures and Comparative Data
phyloseq-1.38.0 Handling and analysis of high-throughput microbiome census data
phytools-0.7-90 Phylogenetic Tools for Comparative Biology (and Other Things)
pillar-1.6.4 Coloured Formatting for Columns
pim-2.0.2 Fit Probabilistic Index Models
pinfsc50-1.2.0 Sequence (‘FASTA’), Annotation (‘GFF’) and Variants (‘VCF’) for 17 Samples of ‘P. Infestans” and 1 ‘P. Mirabilis’
pixmap-0.4-12 Bitmap Images / Pixel Maps
pkgbuild-1.2.0 Find Tools Needed to Build R Packages
pkgconfig-2.0.3 Private Configuration for ‘R’ Packages
pkgload-1.2.3 Simulate Package Installation and Attach
pkgmaker-0.32.2 Development Utilities for R Packages
plogr-0.2.0 The ‘plog’ C++ Logging Library
plot3D-1.4 Plotting Multi-Dimensional Data
plot3Drgl-1.0.2 Plotting Multi-Dimensional Data - Using ‘rgl’
plotly-4.10.0 Create Interactive Web Graphics via ‘plotly.js’
plotmo-3.6.1 Plot a Model’s Residuals, Response, and Partial Dependence Plots
plotrix-3.8-2 Various Plotting Functions
pls-2.8-0 Partial Least Squares and Principal Component Regression
plyr-1.8.6 Tools for Splitting, Applying and Combining Data
png-0.1-7 Read and write PNG images
poLCA-1.4.1 Polytomous variable Latent Class Analysis
poisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distribution
polspline-1.1.19 Polynomial Spline Routines
polyclip-1.10-0 Polygon Clipping
polycor-0.7-10 Polychoric and Polyserial Correlations
polyester-1.30.0 Simulate RNA-seq reads
polynom-1.4-0 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
posterior-1.1.0 Tools for Working with Posterior Distributions
poweRlaw-0.70.6 Analysis of Heavy Tailed Distributions
prabclus-2.3-2 Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data
pracma-2.3.3 Practical Numerical Math Functions
praise-1.0.0 Praise Users
premessa 0.2.6
preprocessCore-1.56.0 A collection of pre-processing functions
preseqR-4.0.0 Predicting Species Accumulation Curves
prettyunits-1.1.1 Pretty, Human Readable Formatting of Quantities
processx-3.5.2 Execute and Control System Processes
prodlim-2019.11.13 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
progress-1.2.2 Terminal Progress Bars
progressr-0.9.0 An Inclusive, Unifying API for Progress Updates
projpred-2.0.2 Projection Predictive Feature Selection
promises-1.2.0.1 Abstractions for Promise-Based Asynchronous Programming
proto-1.0.0 Prototype Object-Based Programming
proxy-0.4-26 Distance and Similarity Measures
pryr-0.1.5 Tools for Computing on the Language
ps-1.6.0 List, Query, Manipulate System Processes
pscl-1.5.5 Political Science Computational Laboratory
pspline-1.0-18 Penalized Smoothing Splines
psych-2.1.9 Procedures for Psychological, Psychometric, and Personality Research
psychotools-0.7-0 Psychometric Modeling Infrastructure
pulsar-0.3.7 Parallel Utilities for Lambda Selection along a Regularization Path
purrr-0.3.4 Functional Programming Tools
pvclust-2.2-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
qdapRegex-0.7.2 Regular Expression Removal, Extraction, and Replacement Tools
qgam-1.3.3 Smooth Additive Quantile Regression Models
qgraph-1.9 Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
qpdf-1.1 Split, Combine and Compress PDF Files
qqman-0.1.8 Q-Q and Manhattan Plots for GWAS Data
qrnn-2.0.5 Quantile Regression Neural Network
qtl-1.50 Tools for Analyzing QTL Experiments
quadprog-1.5-8 Functions to Solve Quadratic Programming Problems
quantmod-0.4.18 Quantitative Financial Modelling Framework
quantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimes
quantreg-5.86 Quantile Regression
quantsmooth-1.60.0 Quantile smoothing and genomic visualization of array data
questionr-0.7.5 Functions to Make Surveys Processing Easier
qvalue-2.26.0 Q-value estimation for false discovery rate control
qvcalc-1.0.2 Quasi Variances for Factor Effects in Statistical Models
r2d3-0.2.5 Interface to ‘D3’ Visualizations
rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
rGADEM-2.42.0 de novo motif discovery
rJava-1.0-5 Low-Level R to Java Interface
rainbow-3.6 Bagplots, Boxplots and Rainbow Plots for Functional Data
randomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and Regression
randomForestSRC-2.13.0 Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
rangeModelMetadata-0.1.4 Provides Templates for Metadata Files Associated with Species Range Models
ranger-0.13.1 A Fast Implementation of Random Forests
rappdirs-0.3.3 Application Directories: Determine Where to Save Data, Caches, and Logs
raster-3.5-2 Geographic Data Analysis and Modeling
rasterVis-0.51.0 Visualization Methods for Raster Data
ratelimitr-0.4.1 Rate Limiting for R
rbenchmark-1.0.0 Benchmarking routine for R
rbibutils-2.2.4 Read ‘Bibtex’ Files and Convert Between Bibliography Formats
rbison-1.0.0 Interface to the ‘USGS’ ‘BISON’ API
rcmdcheck-1.4.0 Run ‘R CMD check’ from ‘R’ and Capture Results
rda-1.0.2-2.1 Shrunken Centroids Regularized Discriminant Analysis
rdrop2-0.8.2.1 Programmatic Interface to the ‘Dropbox’ API
readODS-1.7.0 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-2.0.2 Read Rectangular Text Data
readxl-1.3.1 Read Excel Files
rebird-1.3.0 R Client for the eBird Database of Bird Observations
recipes-0.1.17 Preprocessing and Feature Engineering Steps for Modeling
refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from ‘Ensembl’ and ‘UCSC’ Genome Browsers
refund-0.1-24 Regression with Functional Data
regioneR-1.26.0 Association analysis of genomic regions based on permutation tests
registry-0.5-1 Infrastructure for R Package Registries
regress-1.3-21 Gaussian Linear Models with Linear Covariance Structure
regsem-1.8.0 Regularized Structural Equation Modeling
regtools-1.1.0 Regression and Classification Tools
relations-0.6-10 Data Structures and Algorithms for Relations
relevent-1.1 Relational Event Models
rematch-1.0.1 Match Regular Expressions with a Nicer ‘API’
rematch2-2.1.2 Tidy Output from Regular Expression Matching
remotes-2.4.1 R Package Installation from Remote Repositories, Including ‘GitHub’
rentrez-1.2.3 ‘Entrez’ in R
repr-1.1.3 Serializable Representations
reprex-2.0.1 Prepare Reproducible Example Code via the Clipboard
resample-0.4 Resampling Functions
reshape-0.8.8 Flexibly Reshape Data
reshape2-1.4.4 Flexibly Reshape Data: A Reboot of the Reshape Package
restfulr-0.0.13 R Interface to RESTful Web Services
reticulate-1.22 Interface to ‘Python’
rex-1.2.0 Friendly Regular Expressions
rgbif-3.6.0 Interface to the Global ‘Biodiversity’ Information Facility API
rgdal-1.5-27 Bindings for the ‘Geospatial’ Data Abstraction Library
rgenoud-5.8-3.0 R Version of GENetic Optimization Using Derivatives
rgeos-0.5-8 Interface to Geometry Engine - Open Source (‘GEOS’)
rgexf-0.16.2 Build, Import and Export GEXF Graph Files
rgl-0.107.14 3D Visualization Using OpenGL
rhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Library
rhdf5-2.38.0 R Interface to HDF5
rhdf5filters-1.6.0 HDF5 Compression Filters
ridigbio-0.3.5 Interface to the iDigBio Data API
rio-0.5.27 A Swiss-Army Knife for Data I/O
ritis-1.0.0 Integrated Taxonomic Information System Client
rjags-4-12 Bayesian Graphical Models using MCMC
rjson-0.2.20 JSON for R
rlang-0.4.12 Functions for Base Types and Core R and ‘Tidyverse’ Features
rle-0.9.2 Common Functions for Run-Length Encoded Vectors
rlecuyer-0.3-5 R Interface to RNG with Multiple Streams
rlist-0.4.6.2 A Toolbox for Non-Tabular Data Manipulation
rmarkdown-2.11 Dynamic Documents for R
rmeta-3.0 Meta-Analysis
rms-6.2-0 Regression Modeling Strategies
rncl-0.8.4 An Interface to the Nexus Class Library
rnetcarto-0.2.4 Fast Network Modularity and Roles Computation by Simulated Annealing (Rgraph C Library Wrapper for R)
rngtools-1.5.2 Utility Functions for Working with Random Number Generators
robustbase-0.93-9 Basic Robust Statistics
rootSolve-1.8.2.3 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
rotl-3.0.11 Interface to the ‘Open Tree of Life’ API
roxygen2-7.1.2 In-Line Documentation for R
rpart-4.1-15 Recursive Partitioning and Regression Trees
rprojroot-2.0.2 Finding Files in Project Subdirectories
rrcov-1.6-0 Scalable Robust Estimators with High Breakdown Point
rredlist-0.7.0 ‘IUCN’ Red List Client
rsample-0.1.1 General Resampling Infrastructure
rsconnect-0.8.24 Deployment Interface for R Markdown Documents and Shiny Applications
rslurm-0.6.1 Submit R Calculations to a ‘Slurm’ Cluster
rstan-2.21.2 R Interface to Stan
rstanarm-2.21.1 Bayesian Applied Regression Modeling via Stan
rstantools-2.1.1 Tools for Developing R Packages Interfacing with ‘Stan’
rstatix-0.7.0 Pipe-Friendly Framework for Basic Statistical Tests
rstudioapi-0.13 Safely Access the RStudio API
rsvd-1.0.5 Randomized Singular Value Decomposition
rsvg-2.1.2 Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
rtracklayer-1.54.0 R interface to genome annotation files and the UCSC genome browser
ruv-0.9.7.1 Detect and Remove Unwanted Variation using Negative Controls
rvcheck-0.2.1 R/Package Version Check
rversions-2.1.1 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
rvertnet-0.8.2 Search ‘Vertnet’, a ‘Database’ of Vertebrate Specimen Records
rvest-1.0.2 Easily Harvest (Scrape) Web Pages
rzmq-0.9.8 R Bindings for ‘ZeroMQ’
s2-1.0.7 Spherical Geometry Operators Using the S2 Geometry Library
sampling-2.9 Survey Sampling
samr-3.0 SAM: Significance Analysis of Microarrays
sandwich-3.0-1 Robust Covariance Matrix Estimators
sass-0.4.0 Syntactically Awesome Style Sheets (‘Sass’)
scales-1.1.1 Scale Functions for Visualization
scater-1.22.0 Single-Cell Analysis Toolkit for Gene Expression Data in R
scattermore-0.7 Scatterplots with More Points
scatterpie-0.1.7 Scatter Pie Plot
scatterplot3d-0.3-41 3D Scatter Plot
schoolmath-0.4 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
sctransform-0.3.2 Variance Stabilizing Transformations for Single Cell UMI Data
scuttle-1.4.0 Single-Cell RNA-Seq Analysis Utilities
seewave-2.1.8 Sound Analysis and Synthesis
segmented-1.3-4 Regression Models with Break-Points / Change-Points Estimation
selectr-0.4-2 Translate CSS Selectors to XPath Expressions
sem-3.1-13 Structural Equation Models
semPLS-1.0-10 Structural Equation Modeling Using Partial Least Squares
sendmailR-1.2-1 send email using R
sensemakr-0.1.4 Sensitivity Analysis Tools for Regression Models
seqLogo-1.60.0 Sequence logos for DNA sequence alignments
seqinr-4.2-8 Biological Sequences Retrieval and Analysis
seqminer-8.2 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
sequenza-3.0.0 Copy Number Estimation from Tumor Genome Sequencing Data
servr-0.23 A Simple HTTP Server to Serve Static Files or Dynamic Documents
sessioninfo-1.2.0 R Session Information
setRNG-2013.9-1 Set (Normal) Random Number Generator and Seed
sets-1.0-19 Sets, Generalized Sets, Customizable Sets and Intervals
sf-1.0-3 Simple Features for R
sfsmisc-1.1-12 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
shadowtext-0.0.9 Shadow Text Grob and Layer
shape-1.4.6 Functions for Plotting Graphical Shapes, Colors
shapefiles-0.7 Read and Write ESRI Shapefiles
shiny-1.7.1 Web Application Framework for R
shinyBS-0.61 Twitter Bootstrap Components for Shiny
shinyFiles-0.9.1 A Server-Side File System Viewer for Shiny
shinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s Recalculating
shinydashboard-0.7.2 Create Dashboards with ‘Shiny’
shinyjs-2.0.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
shinystan-2.5.0 Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
shinythemes-1.2.0 Themes for Shiny
siggenes-1.68.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
signal-0.7-7 Signal Processing
sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header Files
slam-0.1-48 Sparse Lightweight Arrays and Matrices
slider-0.2.2 Sliding Window Functions
sm-2.2-5.7 Smoothing Methods for Nonparametric Regression and Density Estimation
smoother-1.1 Functions Relating to the Smoothing of Numerical Data
sn-2.0.0 The Skew-Normal and Related Distributions Such as the Skew-t and the SUN
sna-2.6 Tools for Social Network Analysis
snow-0.4-4 Simple Network of Workstations
snowfall-1.84-6.1 Easier cluster computing (based on snow).
snpStats-1.44.0 SnpMatrix and XSnpMatrix classes and methods
sodium-1.2.0 A Modern and Easy-to-Use Crypto Library
solrium-1.2.0 General Purpose R Interface to ‘Solr’
som-0.3-5.1 Self-Organizing Map
soundecology-1.3.3 Soundscape Ecology
sourcetools-0.1.7 Tools for Reading, Tokenizing and Parsing R Code
sp-1.4-5 Classes and Methods for Spatial Data
spData-2.0.1 Datasets for Spatial Analysis
spThin-0.2.0 Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models
spaMM-3.9.13 Mixed-Effect Models, with or without Spatial Random Effects
spaa-0.2.2 SPecies Association Analysis
spam-2.7-0 SPArse Matrix
sparklyr-1.7.2 R Interface to Apache Spark
sparseMatrixStats-1.6.0 Summary Statistics for Rows and Columns of Sparse Matrices
spatial-7.3-14 Functions for Kriging and Point Pattern Analysis
spatstat-2.2-0 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
spatstat.core-2.3-0 Core Functionality of the ‘spatstat’ Family
spatstat.data-2.1-0 Datasets for ‘spatstat’ Family
spatstat.geom-2.3-0 Geometrical Functionality of the ‘spatstat’ Family
spatstat.linnet-2.3-0 Linear Networks Functionality of the ‘spatstat’ Family
spatstat.sparse-2.0-0 Sparse Three-Dimensional Arrays and Linear Algebra Utilities
spatstat.utils-2.2-0 Utility Functions for ‘spatstat’
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-1.2.0 Interface to Species Occurrence Data Sources
sqldf-0.4-11 Manipulate R Data Frames Using SQL
squash-1.0.9 Color-Based Plots for Multivariate Visualization
ssgraph-1.12 Bayesian Graphical Estimation using Spike-and-Slab Priors
stabledist-0.7-1 Stable Distribution Functions
stabs-0.6-4 Stability Selection with Error Control
stargazer-5.2.2 Well-Formatted Regression and Summary Statistics Tables
startupmsg-0.9.6 Utilities for Start-Up Messages
statmod-1.4.36 Statistical Modeling
statnet-2019.6 Software Tools for the Statistical Analysis of Network Data
statnet.common-4.5.0 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-0.9.8 Approximate String Matching, Fuzzy Text Search, and String Distance Functions
stringi-1.7.5 Character String Processing Facilities
stringr-1.4.0 Simple, Consistent Wrappers for Common String Operations
strucchange-1.5-2 Testing, Monitoring, and Dating Structural Changes
styler-1.6.2 Non-Invasive Pretty Printing of R Code
subplex-1.6 Unconstrained Optimization using the Subplex Algorithm
survey-4.1-1 Analysis of Complex Survey Samples
survival-3.2-13 Survival Analysis
survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
sva-3.42.0 Surrogate Variable Analysis
svd-0.5 Interfaces to Various State-of-Art SVD and Eigensolvers
symmoments-1.2.1 Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution
sys-3.4 Powerful and Reliable Tools for Running System Commands in R
systemPipeR-2.0.1 systemPipeR: NGS workflow and report generation environment
systemfonts-1.0.3 System Native Font Finding
tableone-0.13.0 Create ‘Table 1’ to Describe Baseline Characteristics with or without Propensity Score Weights
tables-0.9.6 Formula-Driven Table Generation
taxize-0.9.99 Taxonomic Information from Around the Web
tcltk built in
tcltk2-1.2-11 Tcl/Tk Additions
tclust-1.4-2 Robust Trimmed Clustering
tensor-1.5 Tensor product of arrays
tensorA-0.36.2 Advanced Tensor Arithmetic with Named Indices
tergm-4.0.2 Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
tergmLite-2.5.5 Fast Simulation of Simple Temporal Exponential Random Graph Models
terra-1.4-11 Spatial Data Analysis
testit-0.13 A Simple Package for Testing R Packages
testthat-3.1.0 Unit Testing for R
threejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globes
tibble-3.1.5 Simple Data Frames
tictoc-1.0.1 Functions for Timing R Scripts, as Well as Implementations of Stack and List Structures
tidygraph-1.2.0 A Tidy API for Graph Manipulation
tidymodels-0.1.4 Easily Install and Load the ‘Tidymodels’ Packages
tidyposterior-0.1.0 Bayesian Analysis to Compare Models using Resampling Statistics
tidypredict-0.4.8 Run Predictions Inside the Database
tidyr-1.1.4 Tidy Messy Data
tidyselect-1.1.1 Select from a Set of Strings
tidytext-0.3.2 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Tools
tidytree-0.3.6 A Tidy Tool for Phylogenetic Tree Data Manipulation
tidyverse-1.3.1 Easily Install and Load the ‘Tidyverse’
tiff-0.1-8 Read and Write TIFF Images
tilingArray-1.72.0 Transcript mapping with high-density oligonucleotide tiling arrays
timeDate-3043.102 Rmetrics - Chronological and Calendar Objects
timeSeries-3062.100 Financial Time Series Objects (Rmetrics)
timereg-2.0.1 Flexible Regression Models for Survival Data
tinytex-0.34 Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
tkWidgets-1.72.0 R based tk widgets
tkrplot-0.0-26 TK Rplot
tm-0.7-8 Text Mining Package
tmle-1.5.0.2 Targeted Maximum Likelihood Estimation
tmvnsim-1.0-2 Truncated Multivariate Normal Simulation
tmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distribution
tokenizers-0.2.1 Fast, Consistent Tokenization of Natural Language Text
tools built in
topicmodels-0.2-12 Topic Models
tree-1.0-41 Classification and Regression Trees
treeio-1.18.1 Base Classes and Functions for Phylogenetic Tree Input and Output
triebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’
trimcluster-0.1-5 Cluster Analysis with Trimming
tripack-1.3-9.1 Triangulation of Irregularly Spaced Data
truncnorm-1.0-8 Truncated Normal Distribution
trust-0.1-8 Trust Region Optimization
tseries-0.10-48 Time Series Analysis and Computational Finance
tseriesChaos-0.1-13.1 Analysis of Nonlinear Time Series
tsna-0.3.4 Tools for Temporal Social Network Analysis
tsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
tune-0.1.6 Tidy Tuning Tools
tuneR-1.3.3.1 Analysis of Music and Speech
twang-2.5 Toolkit for Weighting and Analysis of Nonequivalent Groups
tweedie-2.3.3 Evaluation of Tweedie Exponential Family Models
tweenr-1.0.2 Interpolate Data for Smooth Animations
tzdb-0.2.0 Time Zone Database Information
ucminf-1.1-4 General-Purpose Unconstrained Non-Linear Optimization
udunits2-0.13.1 Udunits-2 Bindings for R
unbalanced-2.0 Racing for Unbalanced Methods Selection
uniqueAtomMat-0.1-3-2 Finding Unique or Duplicated Rows or Columns for Atomic Matrices
units-0.7-2 Measurement Units for R Vectors
unmarked-1.1.1 Models for Data from Unmarked Animals
urca-1.3-0 Unit Root and Cointegration Tests for Time Series Data
urltools-1.7.3 Vectorised Tools for URL Handling and Parsing
uroot-2.1-2 Unit Root Tests for Seasonal Time Series
usethis-2.1.3 Automate Package and Project Setup
utf8-1.2.2 Unicode Text Processing
utils built in
uuid-1.0-2 Tools for Generating and Handling of UUIDs
uwot-0.1.10 The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
vcd-1.4-9 Visualizing Categorical Data
vcfR-1.12.0 Manipulate and Visualize VCF Data
vctrs-0.3.8 Vector Helpers
vegan-2.5-7 Community Ecology Package
venn-1.10 Draw Venn Diagrams
vimp-2.2.5 Perform Inference on Algorithm-Agnostic Variable Importance
vioplot-0.3.7 Violin Plot
vipor-0.4.5 Plot Categorical Data Using Quasirandom Noise and Density Estimates
viridis-0.6.2 Colorblind-Friendly Color Maps for R
viridisLite-0.4.0 Colorblind-Friendly Color Maps (Lite Version)
visNetwork-2.1.0 Network Visualization using ‘vis.js’ Library
visdat-0.5.3 Preliminary Visualisation of Data
vroom-1.5.5 Read and Write Rectangular Text Data Quickly
vsn-3.62.0 Variance stabilization and calibration for microarray data
waldo-0.3.1 Find Differences Between R Objects
warp-0.2.0 Group Dates
waveslim-1.8.2 Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing
wavethresh-4.6.8 Wavelets Statistics and Transforms
webp-1.1.0 A New Format for Lossless and Lossy Image Compression
webshot-0.5.2 Take Screenshots of Web Pages
wellknown-0.7.4 Convert Between ‘WKT’ and ‘GeoJSON’
whisker-0.4 for R, Logicless Templating
widgetTools-1.72.0 Creates an interactive tcltk widget
wikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’
withr-2.4.2 Run Code ‘With’ Temporarily Modified Global State
wk-0.5.0 Lightweight Well-Known Geometry Parsing
wordcloud-2.6 Word Clouds
workflows-0.2.4 Modeling Workflows
workflowsets-0.1.0 Create a Collection of ‘tidymodels’ Workflows
worrms-0.4.2 World Register of Marine Species (WoRMS) Client
xCell 1.1.0
xfun-0.27 Supporting Functions for Packages Maintained by ‘Yihui Xie’
xgboost-1.4.1.1 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
xml2-1.3.2 Parse XML
xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Tree
xopen-1.0.0 Open System Files, ‘URLs’, Anything
xtable-1.8-4 Export Tables to LaTeX or HTML
xts-0.12.1 eXtensible Time Series
yaImpute-1.0-32 Nearest Neighbor Observation Imputation and Evaluation Tools
yaml-2.2.1 Methods to Convert R Data to YAML and Back
yardstick-0.0.9 Tidy Characterizations of Model Performance
yulab.utils-0.0.4 Supporting Functions for Packages Maintained by ‘YuLab-SMU’
zCompositions-1.3.4 Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
zeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignment
zip-2.2.0 Cross-Platform ‘zip’ Compression
zlibbioc-1.40.0 An R packaged zlib-1.2.5
zoo-1.8-9 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)

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