fhR-4.0.2-foss-2019b

Fred Hutch R

R with addition libraries from user requests. This release has a new name, placing ‘fh’ as a prefix. Two modules are created for each R version. A base R module suited to general purpose use which contains over 700 libraries. libraries. The Fred Hutch R is a superset of the base R module plus addition libraries.

Known Issues

Replaces R-4.0.1 which has memory issues. R-4.0.2 is a quick release to fix issues with 4.0.1. Usage of 4.0.1 is discouraged.

Package List

ADGofTest-0.3 Anderson-Darling GoF test
ALDEx2-1.20.0 Analysis Of Differential Abundance Taking Sample Variation Into Account
ALL-1.30.0 A data package
ASCAT 2.5.2
AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.
AgiMicroRna-2.38.0 Processing and Differential Expression Analysis of Agilent microRNA chips
AlgDesign-1.2.0 Algorithmic Experimental Design
AnnotationDbi-1.50.1 Manipulation of SQLite-based annotations in Bioconductor
AnnotationFilter-1.12.0 Facilities for Filtering Bioconductor Annotation Resources
AnnotationForge-1.30.1 Tools for building SQLite-based annotation data packages
AnnotationHub-2.20.0 Client to access AnnotationHub resources
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-2.62 Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
BH-1.72.0-3 Boost C++ Header Files
BMA-3.18.12 Bayesian Model Averaging
BSgenome-1.56.0 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-2.48.0 Biobase: Base functions for Bioconductor
BiocFileCache-1.12.0 Manage Files Across Sessions
BiocGenerics-0.34.0 S4 generic functions used in Bioconductor
BiocManager-1.30.10 Access the Bioconductor Project Package Repository
BiocParallel-1.22.0 Bioconductor facilities for parallel evaluation
BiocStyle-2.16.0 Standard styles for vignettes and other Bioconductor documents
BiocVersion-3.11.1 Set the appropriate version of Bioconductor packages
Biostrings-2.56.0 Efficient manipulation of biological strings
BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
Bolstad-0.2-40 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
CGEN-3.23.0 An R package for analysis of case-control studies in genetic epidemiology
CGHbase-1.48.0 CGHbase: Base functions and classes for arrayCGH data analysis.
COMPASS-1.26.0 Combinatorial Polyfunctionality Analysis of Single Cells
CVST-0.2-2 Fast Cross-Validation via Sequential Testing
Cairo-1.5-12 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-2.54.0 Category Analysis
ChIPpeakAnno-3.22.2 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
ComICS-1.0.4 Computational Methods for Immune Cell-Type Subsets
CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
ConsensusClusterPlus-1.52.0 ConsensusClusterPlus
CovSel-1.2.1 Model-Free Covariate Selection
CytoML-2.0.5 A GatingML Interface for Cross Platform Cytometry Data Sharing
DAAG-1.24 Data Analysis and Graphics Data and Functions
DBI-1.1.0 R Database Interface
DEGseq-1.42.0 Identify Differentially Expressed Genes from RNA-seq data
DESeq-1.39.0 Differential gene expression analysis based on the negative binomial distribution
DESeq2-1.28.1 Differential gene expression analysis based on the negative binomial distribution
DEoptimR-1.0-8 Differential Evolution Optimization in Pure R
DHARMa-0.3.2.0 Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
DNAcopy-1.62.0 DNA copy number data analysis
DOT-0.1 Render and Export DOT Graphs in R
DRR-0.0.4 Dimensionality Reduction via Regression
DT-0.14 A Wrapper of the JavaScript Library ‘DataTables’
DTRreg-1.5 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
DelayedArray-0.14.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
DelayedMatrixStats-1.10.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
Deriv-4.0 Symbolic Differentiation
DiagrammeR-1.0.6.1 Graph/Network Visualization
DiceDesign-1.8-1 Designs of Computer Experiments
DiffBind-2.16.0 Differential Binding Analysis of ChIP-Seq Peak Data
DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
DistributionUtils-0.6-0 Distribution Utilities
DynDoc-1.66.0 Dynamic document tools
EBImage-4.30.0 Image processing and analysis toolbox for R
EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
EpiModel-1.8.0 Mathematical Modeling of Infectious Disease Dynamics
FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
FME-1.3.6.1 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-2.3 Multivariate Exploratory Data Analysis and Data Mining
FlowSOM-1.20.0 Using self-organizing maps for visualization and interpretation of cytometry data
Formula-1.2-3 Extended Model Formulas
GENESIS-2.18.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GEOquery-2.56.0 Get data from NCBI Gene Expression Omnibus (GEO)
GGally-2.0.0 Extension to ‘ggplot2’
GO.db-3.11.4 A set of annotation maps describing the entire Gene Ontology
GOstats-2.54.0 Tools for manipulating GO and microarrays
GPfit-1.0-8 Gaussian Processes Modeling
GSA-1.03.1 Gene Set Analysis
GSEABase-1.50.1 Gene set enrichment data structures and methods
GSVA-1.36.2 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-1.34.0 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-1.24.2 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
GenomeInfoDbData-1.2.3 Species and taxonomy ID look up tables used by GenomeInfoDb
GenomicAlignments-1.24.0 Representation and manipulation of short genomic alignments
GenomicFeatures-1.40.0 Conveniently import and query gene models
GenomicFiles-1.24.0 Distributed computing by file or by range
GenomicRanges-1.40.0 Representation and manipulation of genomic intervals
GetoptLong-1.0.0 Parsing Command-Line Arguments and Simple Variable Interpolation
GillespieSSA-0.6.1 Gillespie’s Stochastic Simulation Algorithm (SSA)
Glimma-1.16.0 Interactive HTML graphics
GlobalOptions-0.1.2 Generate Functions to Get or Set Global Options
Gviz-1.32.0 Plotting data and annotation information along genomic coordinates
HCsnip 1.2.0
HDF5Array-1.16.1 HDF5 backend for DelayedArray objects
HMMcopy-1.30.0 Copy number prediction with correction for GC and mappability bias for HTS data
HSMMSingleCell-1.8.0 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-1.8-11 Hidden Markov Models
Hmisc-4.4-0 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)’
IDSpatialStats-0.3.10 Estimate Global Clustering in Infectious Disease
IHW-1.16.0 Independent Hypothesis Weighting
IRanges-2.22.2 Foundation of integer range manipulation in Bioconductor
IRdisplay-0.7.0 ‘Jupyter’ Display Machinery
ISOcodes-2020.03.16 Selected ISO Codes
IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
Iso-0.0-18.1 Functions to Perform Isotonic Regression
JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J. Buttlar
KEGG.db-3.2.4 A set of annotation maps for KEGG
KEGGREST-1.28.0 Client-side REST access to KEGG
KEGGgraph-1.48.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGprofile-1.30.0 An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
KODAMA-1.5 Knowledge Discovery by Accuracy Maximization
KernSmooth-2.23-17 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
LaplacesDemon-16.1.4 Complete Environment for Bayesian Inference
LearnBayes-2.15.1 Functions for Learning Bayesian Inference
Lmoments-1.3-1 L-Moments and Quantile Mixtures
LogicReg-1.6.2 Logic Regression
LymphoSeq-1.16.0 Analyze high-throughput sequencing of T and B cell receptors
LymphoSeqDB-0.99.2 LymphoSeq annotation databases
MALDIquant-1.19.3 Quantitative Analysis of Mass Spectrometry Data
MASS-7.3-51.6 Support Functions and Datasets for Venables and Ripley’s MASS
MCMCglmm-2.29 MCMC Generalised Linear Mixed Models
MCMCpack-1.4-8 Markov Chain Monte Carlo (MCMC) Package
MIIVsem-0.5.5 Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
MPV-1.55 Data Sets from Montgomery, Peck and Vining
MatchIt-3.0.2 Nonparametric Preprocessing for Parametric Causal Inference
Matching-4.9-7 Multivariate and Propensity Score Matching with Balance Optimization
Matrix-1.2-18 Sparse and Dense Matrix Classes and Methods
MatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
MatrixModels-0.4-1 Modelling with Sparse And Dense Matrices
Mfuzz-2.48.0 Soft clustering of time series gene expression data
ModelMetrics-1.2.2.2 Rapid Calculation of Model Metrics
MotIV-1.43.0 Motif Identification and Validation
NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
NLP-0.2-0 Natural Language Processing Infrastructure
NOISeq-2.31.0 Exploratory analysis and differential expression for RNA-seq data
OceanView-1.0.5 Visualisation of Oceanographic Data and Model Output
OrganismDbi-1.30.0 Software to enable the smooth interfacing of different database packages
PBSddesolve-1.12.6 Solver for Delay Differential Equations
PFAM.db-3.11.4 A set of protein ID mappings for PFAM
PICS-2.32.0 Probabilistic inference of ChIP-seq
PKI-0.1-7 Public Key Infrastucture for R Based on the X.509 Standard
ParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
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-1.20.0 S4 generic functions for Bioconductor proteomics infrastructure
R.cache-0.14.0 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.methodsS3-1.8.0 S3 Methods Simplified
R.oo-1.23.0 R Object-Oriented Programming with or without References
R.rsp-0.43.2 Dynamic Generation of Scientific Reports
R.utils-2.9.2 Various Programming Utilities
R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
R2jags-0.6-1 Using R to Run ‘JAGS’
R6-2.4.1 Encapsulated Classes with Reference Semantics
RANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
RBGL-1.64.0 An interface to the BOOST graph library
RCircos-1.2.1 Circos 2D Track Plot
RColorBrewer-1.1-2 ColorBrewer Palettes
RCurl-1.98-1.2 General Network (HTTP/FTP/…) Client Interface for R
REDCapR-0.11.0 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-1.3-1.4 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<U+000a>Theory
RNASeqPower-1.28.0 Sample size for RNAseq studies
RNeXML-2.4.5 Semantically Rich I/O for the ‘NeXML’ Format
ROCR-1.0-11 Visualizing the Performance of Scoring Classifiers
ROI-0.3-3 R Optimization Infrastructure
ROI.plugin.glpk-0.3-0 ‘ROI’ Plug-in ‘GLPK’
RPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database System
RProtoBufLib-2.0.0 C++ headers and static libraries of Protocol buffers
RSNNS-0.4-12 Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
RSQLite-2.2.0 ‘SQLite’ Interface for R
RSclient-0.7-3 Client for Rserve
RSpectra-0.16-0 Solvers for Large-Scale Eigenvalue and SVD Problems
RUnit-0.4.32 R Unit Test Framework
RWeka-0.4-42 R/Weka Interface
RWekajars-3.9.3-2 R/Weka Interface Jars
Rborist-0.2-3 Extensible, Parallelizable Implementation of the Random Forest Algorithm
Rcpp-1.0.4.6 Seamless R and C++ Integration
RcppAnnoy-0.0.16 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest Neighbors
RcppArmadillo-0.9.900.1.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library
RcppEigen-0.3.3.7.0 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra Library
RcppGSL-0.3.8 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and Matrices
RcppParallel-5.0.2 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
Rdpack-1.0.0 Update and Manipulate Rd Documentation Objects
Rdsdp-1.0.5 R Interface to DSDP Semidefinite Programming Library
ReportingTools-2.28.0 Tools for making reports in various formats
Rglpk-0.6-4 R/GNU Linear Programming Kit Interface
Rgraphviz-2.32.0 Provides plotting capabilities for R graph objects
Rhdf5lib-1.10.0 hdf5 library as an R package
Rhpc-0.19-276 Permits *apply() Style Dispatch for ‘HPC’
Rhtslib-1.20.0 HTSlib high-throughput sequencing library as an R package
Ringo-1.52.0 R Investigation of ChIP-chip Oligoarrays
Rlabkey-2.5.0 Data Exchange Between R and ‘LabKey’ Server
Rmpi-0.6-9 Interface (Wrapper) to MPI (Message-Passing Interface)
Rook-1.1-1 Rook - a web server interface for R
Rsamtools-2.4.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Rserve-1.7-3.1 Binary R server
Rssa-1.0.2 A Collection of Methods for Singular Spectrum Analysis
Rsubread-2.2.2 Subread Sequence Alignment and Counting for R
Rtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
Rttf2pt1-1.3.8 ‘ttf2pt1’ Program
S4Vectors-0.26.1 Foundation of vector-like and list-like containers in Bioconductor
SDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
SKAT-2.0.0 SNP-Set (Sequence) Kernel Association Test
SNPRelate-1.22.0 Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)
SOAR-0.99-11 Memory management in R by delayed assignments
SPAtest-3.0.2 Score Test and Meta-Analysis Based on Saddlepoint Approximation
SPIA-2.40.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
SQUAREM-2020.3 Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
SemiPar-1.0-4.2 Semiparametic Regression
SeqArray-1.28.1 Data management of large-scale whole-genome sequence variant calls
SeqVarTools-1.26.0 Tools for variant data
Seurat-3.1.5 Tools for Single Cell Genomics
ShortRead-1.46.0 FASTQ input and manipulation
SignifReg-3.0 Consistent Significance Controlled Variable Selection in Linear Regression
SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
SnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 Library
SparseM-1.78 Sparse Linear Algebra
StanHeaders-2.21.0-5 C++ Header Files for Stan
SummarizedExperiment-1.18.1 SummarizedExperiment container
SuperLearner-2.0-26 Super Learner Prediction
SuppDists-1.1-9.5 Supplementary Distributions
TFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination Method
TH.data-1.0-10 TH’s Data Archive
TMB-1.7.16 Template Model Builder: A General Random Effect Tool Inspired by ‘ADMB’
TTR-0.23-6 Technical Trading Rules
TeachingDemos-2.12 Demonstrations for Teaching and Learning
TitanCNA-1.26.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
TraMineR-2.2-0.1 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
V8-3.2.0 Embedded JavaScript and WebAssembly Engine for R
VGAM-1.1-3 Vector Generalized Linear and Additive Models
VIM-6.0.0 Visualization and Imputation of Missing Values
VSURF-1.1.0 Variable Selection Using Random Forests
VariantAnnotation-1.34.0 Annotation of Genetic Variants
VennDiagram-1.6.20 Generate High-Resolution Venn and Euler Plots
WikidataR-1.4.0 API Client Library for ‘Wikidata’
WikipediR-1.5.0 A MediaWiki API Wrapper
Wrench-1.6.0 Wrench normalization for sparse count data
WriteXLS-5.0.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files
XML-3.99-0.3 Tools for Parsing and Generating XML Within R and S-Plus
XVector-0.28.0 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
ade4-1.7-15 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
admisc-0.8 Adrian Dusa’s Miscellaneous
affy-1.66.0 Methods for Affymetrix Oligonucleotide Arrays
affycoretools-1.60.1 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
affyio-1.58.0 Tools for parsing Affymetrix data files
aggregation-1.0.1 p-Value Aggregation Methods
akima-0.6-2.1 Interpolation of Irregularly and Regularly Spaced Data
alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
amap-0.8-18 Another Multidimensional Analysis Package
animation-2.6 A Gallery of Animations in Statistics and Utilities to Create Animations
annaffy-1.60.0 Annotation tools for Affymetrix biological metadata
annotate-1.66.0 Annotation for microarrays
aod-1.3.1 Analysis of Overdispersed Data
ape-5.4 Analyses of Phylogenetics and Evolution
aplot-0.0.4 Decorate a ‘ggplot’ with Associated Information
argparse-2.0.1 Command Line Optional and Positional Argument Parser
argparser-0.6 Command-Line Argument Parser
arm-1.11-1 Data Analysis Using Regression and Multilevel/Hierarchical Models
askpass-1.1 Safe Password Entry for R, Git, and SSH
asnipe-1.1.12 Animal Social Network Inference and Permutations for Ecologists
assertthat-0.2.1 Easy Pre and Post Assertions
audio-0.1-7 Audio Interface for R
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
backports-1.1.8 Reimplementations of Functions Introduced Since R-3.0.0
bacr-1.0.1 Bayesian Adjustment for Confounding
bartMachine-1.2.4.2 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
batchtools-0.9.13 Tools for Computation on Batch Systems
baySeq-2.22.0 Empirical Bayesian analysis of patterns of differential expression in count data
bayesm-3.1-4 Bayesian Inference for Marketing/Micro-Econometrics
bayesplot-1.7.2 Plotting for Bayesian Models
bbmle-1.0.23.1 Tools for General Maximum Likelihood Estimation
bdsmatrix-1.3-4 Routines for Block Diagonal Symmetric Matrices
beanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)
beeswarm-0.2.3 The Bee Swarm Plot, an Alternative to Stripchart
benchmark-0.3-6 Benchmark Experiments Toolbox
bibtex-0.4.2.2 Bibtex Parser
biglm-0.9-2 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-2.4-1 Biological Structure Analysis
biom-0.3.12 An interface package (beta) for the BIOM file format.
biomaRt-2.44.1 Interface to BioMart databases (i.e. Ensembl)
biovizBase-1.36.0 Basic graphic utilities for visualization of genomic data.
bit-1.1-15.2 A Class for Vectors of 1-Bit Booleans
bit64-0.9-7 A S3 Class for Vectors of 64bit Integers
bitops-1.0-6 Bitwise Operations
blob-1.2.1 A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’)
bmp-0.3 Read Windows Bitmap (BMP) Images
bnlearn-4.5 Bayesian Network Structure Learning, Parameter Learning and Inference
bold-1.1.0 Interface to Bold Systems API
bookdown-0.20 Authoring Books and Technical Documents with R Markdown
boot-1.3-25 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-0.6.2 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-1.0-0 Bridge Sampling for Marginal Likelihoods and Bayes Factors
broom-0.5.6 Convert Statistical Analysis Objects into Tidy Tibbles
bst-0.3-21 Gradient Boosting
bumphunter-1.30.0 Bump Hunter
caTools-1.18.0 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
calibrate-1.7.7 Calibration of Scatterplot and Biplot Axes
callr-3.4.3 Call R from R
car-3.0-8 Companion to Applied Regression
carData-3.0-4 Companion to Applied Regression Data Sets
caret-6.0-86 Classification and Regression Training
catdata-1.2.2 Categorical Data
cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
cgdsr-1.3.0 R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)
cghFLasso-0.2-1 Detecting hot spot on CGH array data with fused lasso<U+000a>regression.
checkmate-2.0.0 Fast and Versatile Argument Checks
chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
chipseq-1.38.0 chipseq: A package for analyzing chipseq data
chron-2.3-55 Chronological Objects which can Handle Dates and Times
circlize-0.4.10 Circular Visualization
circular-0.4-93 Circular Statistics
clValid-0.6-8 Validation of Clustering Results
class-7.3-17 Functions for Classification
classInt-0.4-3 Choose Univariate Class Intervals
cli-2.0.2 Helpers for Developing Command Line Interfaces
clipr-0.7.0 Read and Write from the System Clipboard
clisymbols-1.2.0 Unicode Symbols at the R Prompt
clue-0.3-57 Cluster Ensembles
cluster-2.1.0 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al.
clusterGeneration-1.3.4 Random Cluster Generation (with Specified Degree of Separation)
clusterRepro-0.9 Reproducibility of Gene Expression Clusters
clustree-0.4.3 Visualise Clusterings at Different Resolutions
cobs-1.3-4 Constrained B-Splines (Sparse Matrix Based)
coda-0.19-3 Output Analysis and Diagnostics for MCMC
codetools-0.2-16 Code Analysis Tools for R
coin-1.3-1 Conditional Inference Procedures in a Permutation Test Framework
colorspace-1.4-1 A Toolbox for Manipulating and Assessing Colors and Palettes
colourpicker-1.0 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
compositions-1.40-5 Compositional Data Analysis
conditionz-0.1.0 Control How Many Times Conditions are Thrown
config-0.3 Manage Environment Specific Configuration Values
copula-1.0-0 Multivariate Dependence with Copulas
corpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlation
covr-3.5.0 Test Coverage for Packages
cowplot-1.0.0 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
coxme-2.2-16 Mixed Effects Cox Models
crayon-1.3.4 Colored Terminal Output
crosstalk-1.1.0.1 Inter-Widget Interactivity for HTML Widgets
crul-0.9.0 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 Adaptive Multivariate Integration over Hypercubes
cummeRbund-2.30.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
curl-4.3 A Modern and Flexible Web Client for R
cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
cyclocomp-1.1.0 Cyclomatic Complexity of R Code
cytolib-2.0.3 C++ infrastructure for representing and interacting with the gated cytometry
d3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from R
dHSIC-2.1 Independence Testing via Hilbert Schmidt Independence Criterion
dada2-1.16.0 Accurate, high-resolution sample inference from amplicon sequencing data
data.table-1.12.8 Extension of data.frame
datasets built in
dbplyr-1.4.4 A ‘dplyr’ Back End for Databases
ddalpha-1.3.11 Depth-Based Classification and Calculation of Data Depth
deSolve-1.28 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-0.1-25 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
dendextend-1.13.4 Extending ‘dendrogram’ Functionality in R
derfinder-1.22.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
derfinderHelper-1.22.0 derfinder helper package
desc-1.2.0 Manipulate DESCRIPTION Files
descr-1.1.4 Descriptive Statistics
devtools-2.3.0 Tools to Make Developing R Packages Easier
dfidx-0.0-3 Indexed Data Frames
dfoptim-2018.2-1 Derivative-Free Optimization
diagram-1.6.4 Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
dials-0.0.7 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
diffusionMap-1.2.0 Diffusion Map
digest-0.6.25 Create Compact Hash Digests of R Objects
dimRed-0.2.3 A Framework for Dimensionality Reduction
diptest-0.75-7 Hartigan’s Dip Test Statistic for Unimodality - Corrected
dismo-1.1-4 Species Distribution Modeling
distillery-1.0-7 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’
diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis Package
doBy-4.6.6 Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
doMC-1.3.6 Foreach Parallel Adaptor for ‘parallel’
doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
doParallel-1.0.15 Foreach Parallel Adaptor for the ‘parallel’ Package
doRNG-1.8.2 Generic Reproducible Parallel Backend for ‘foreach’ Loops
doSNOW-1.0.18 Foreach Parallel Adaptor for the ‘snow’ Package
dotCall64-1.0-0 Enhanced Foreign Function Interface Supporting Long Vectors
downloader-0.4 Download Files over HTTP and HTTPS
dplyr-1.0.0 A Grammar of Data Manipulation
dqrng-0.2.1 Fast Pseudo Random Number Generators
dr-3.0.10 Methods for Dimension Reduction for Regression
dtangle-2.0.9 Cell Type Deconvolution from Gene Expressions
dtw-1.21-3 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
e1071-1.7-3 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
edgeR-3.30.3 Empirical Analysis of Digital Gene Expression Data in R
elasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCA
ellipse-0.4.2 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
ellipsis-0.3.1 Tools for Working with …
emdbook-1.3.12 Support Functions and Data for “Ecological Models and Data”
emulator-1.2-20 Bayesian Emulation of Computer Programs
energy-1.7-7 E-Statistics: Multivariate Inference via the Energy of Data
ensembldb-2.12.1 Utilities to create and use Ensembl-based annotation databases
entropy-1.2.1 Estimation of Entropy, Mutual Information and Related Quantities
epitools-0.5-10.1 Epidemiology Tools
ergm-3.10.4 Fit, Simulate and Diagnose Exponential-Family Models for Networks
ergm.count-3.4.0 Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
evaluate-0.14 Parsing and Evaluation Tools that Provide More Details than the Default
expm-0.999-4 Matrix Exponential, Log, ‘etc’
expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
extRemes-2.0-12 Extreme Value Analysis
extrafont-0.17 Tools for using fonts
extrafontdb-1.0 Package for holding the database for the extrafont package
fail-1.3 File Abstraction Interface Layer (FAIL)
fansi-0.4.1 ANSI Control Sequence Aware String Functions
faraway-1.0.7 Functions and Datasets for Books by Julian Faraway
farver-2.0.3 High Performance Colour Space Manipulation
fastICA-1.2-2 FastICA Algorithms to Perform ICA and Projection Pursuit
fastcluster-1.1.25 Fast Hierarchical Clustering Routines for R and ‘Python’
fastmap-1.0.1 Fast Implementation of a Key-Value Store
fastmatch-1.1-0 Fast match() function
fastseg-1.34.0 fastseg - a fast segmentation algorithm
fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
fda-5.1.4 Functional Data Analysis
fdrtool-1.2.15 Estimation of (Local) False Discovery Rates and Higher Criticism
feather-0.3.5 R Bindings to the Feather ‘API’
ff-2.2-14.2 Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
ffbase-0.12.8 Basic Statistical Functions for Package ‘ff’
fftw-1.0-6 Fast FFT and DCT Based on the FFTW Library
fftwtools-0.9-8 Wrapper for ‘FFTW3’ Includes: One-Dimensional Univariate, One-Dimensional Multivariate, and Two-Dimensional Transform
fields-10.3 Tools for Spatial Data
filehash-2.4-2 Simple Key-Value Database
findpython-1.0.5 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-0.63 Compare Fitted Models
fitdistrplus-1.1-1 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-2.3-15 Flexible Mixture Modeling
flowClust-3.26.0 Clustering for Flow Cytometry
flowCore-2.0.1 flowCore: Basic structures for flow cytometry data
flowStats-4.0.0 Statistical methods for the analysis of flow cytometry data
flowViz-1.52.0 Visualization for flow cytometry
flowWorkspace-4.0.6 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)
forcats-0.5.0 Tools for Working with Categorical Variables (Factors)
foreach-1.5.0 Provides Foreach Looping Construct
forecast-8.12 Forecasting Functions for Time Series and Linear Models
foreign-0.8-80 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …
forge-0.2.0 Casting Values into Shape
formatR-1.7 Format R Code Automatically
fossil-0.4.0 Palaeoecological and Palaeogeographical Analysis Tools
fpc-2.2-7 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-1.4.2 Cross-Platform File System Operations Based on ‘libuv’
fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
furrr-0.1.0 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-1.17.0 Unified Parallel and Distributed Processing in R for Everyone
future.apply-1.6.0 Apply Function to Elements in Parallel using Futures
gage-2.37.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
gam-1.16.1 Generalized Additive Models
gamlss-5.1-6 Generalised Additive Models for Location Scale and Shape
gamlss.data-5.1-4 GAMLSS Data
gamlss.dist-5.1-6 Distributions for Generalized Additive Models for Location Scale and Shape
gamlss.tr-5.1-0 Generating and Fitting Truncated `gamlss.family’ Distributions
gamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
gap-1.2.2 Genetic Analysis Package
gapfill-0.9.6 Fill Missing Values in Satellite Data
gbRd-0.4-11 Utilities for processing Rd objects and files
gbm-2.1.5 Generalized Boosted Regression Models
gclus-1.3.2 Clustering Graphics
gcrma-2.60.0 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-1.24.1 R Interface to CoreArray Genomic Data Structure (GDS) files
gee-4.13-20 Generalized Estimation Equation Solver
geepack-1.3-1 Generalized Estimating Equation Package
geiger-2.0.7 Analysis of Evolutionary Diversification
geneLenDataBase-1.24.0 Lengths of mRNA transcripts for a number of genomes
genefilter-1.70.0 genefilter: methods for filtering genes from high-throughput experiments
geneplotter-1.66.0 Graphics related functions for Bioconductor
generics-0.0.2 Common S3 Generics not Provided by Base R Methods Related to Model Fitting
genoset-1.44.0 A RangedSummarizedExperiment with methods for copy number analysis
geometry-0.4.5 Mesh Generation and Surface Tessellation
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-1.36.0 Visualization tools for genomic data
ggcyto-1.16.0 Visualize Cytometry data with ggplot
ggforce-0.3.2 Accelerating ‘ggplot2’
ggplot2-3.3.2 Create Elegant Data Visualisations Using the Grammar of Graphics
ggraph-2.0.3 An Implementation of Grammar of Graphics for Graphs and Networks
ggrepel-0.8.2 Automatically Position Non-Overlapping Text Labels with ‘ggplot2’
ggridges-0.5.2 Ridgeline Plots in ‘ggplot2’
ggthemes-4.2.0 Extra Themes, Scales and Geoms for ‘ggplot2’
ggtree-2.2.1 an R package for visualization of tree and annotation data
ggvis-0.4.5 Interactive Grammar of Graphics
gh-1.1.0 ‘GitHub’ ‘API’
git2r-0.27.1 Provides Access to Git Repositories
glasso-1.11 Graphical Lasso: Estimation of Gaussian Graphical Models
gllvm-1.2.2 Generalized Linear Latent Variable Models
glmmML-1.1.1 Generalized Linear Models with Clustering
glmmTMB-1.0.1 Generalized Linear Mixed Models using Template Model Builder
glmnet-4.0-2 Lasso and Elastic-Net Regularized Generalized Linear Models
glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model
globals-0.12.5 Identify Global Objects in R Expressions
glue-1.4.1 Interpreted String Literals
gmm-1.6-5 Generalized Method of Moments and Generalized Empirical Likelihood
gmodels-2.18.1 Various R Programming Tools for Model Fitting
gmp-0.6-0 Multiple Precision Arithmetic
goftest-1.2-2 Classical Goodness-of-Fit Tests for Univariate Distributions
gomms-1.0 GLM-Based Ordination Method
goseq-1.40.0 Gene Ontology analyser for RNA-seq and other length biased data
gower-0.2.2 Gower’s Distance
gplots-3.0.3 Various R Programming Tools for Plotting Data
grDevices built in
grImport2-0.2-0 Importing ‘SVG’ Graphics
graph-1.66.0 graph: A package to handle graph data structures
graphics built in
graphlayouts-0.7.0 Additional Layout Algorithms for Network Visualizations
grid built in
gridBase-0.4-7 Integration of base and grid graphics
gridExtra-2.3 Miscellaneous Functions for “Grid” Graphics
grpreg-3.3.0 Regularization Paths for Regression Models with Grouped Covariates
gsalib-2.1 Utility Functions For GATK
gsl-2.1-6 Wrapper for the Gnu Scientific Library
gsubfn-0.7 Utilities for Strings and Function Arguments
gsw-1.0-5 Gibbs Sea Water Functions
gtable-0.3.0 Arrange ‘Grobs’ in Tables
gtools-3.8.2 Various R Programming Tools
h2o-3.30.0.1 R Interface for the ‘H2O’ Scalable Machine Learning Platform
hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
haplo.stats-1.7.9 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
hardhat-0.1.3 Construct Modeling Packages
haven-2.3.1 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
hdf5r-1.3.2 Interface to the ‘HDF5’ Binary Data Format
hdm-0.3.1 High-Dimensional Metrics
heatmap3-1.1.7 An Improved Heatmap Package
hexbin-1.28.1 Hexagonal Binning Routines
hgu133plus2.db-3.2.3 Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2)
highr-0.8 Syntax Highlighting for R Source Code
hms-0.5.3 Pretty Time of Day
hopach-2.48.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
htmlTable-2.0.0 Advanced Tables for Markdown/HTML
htmltools-0.5.0 Tools for HTML
htmlwidgets-1.5.1 HTML Widgets for R
httpcode-0.3.0 ‘HTTP’ Status Code Helper
httpuv-1.5.4 HTTP and WebSocket Server Library
httr-1.4.1 Tools for Working with URLs and HTTP
huge-1.3.4.1 High-Dimensional Undirected Graph Estimation
hunspell-3.0 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
igraph-1.2.5 Network Analysis and Visualization
igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
illuminaio-0.30.0 Parsing Illumina Microarray Output Files
imager-0.42.3 Image Processing Library Based on ‘CImg’
imagerExtra-1.3.2 Extra Image Processing Library Based on ‘imager’
impute-1.62.0 impute: Imputation for microarray data
ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
infer-0.5.2 Tidy Statistical Inference
inferference-1.0.0 Methods for Causal Inference with Interference
influenceR-0.1.0 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-0.3.15 Functions to Inline C, C++, Fortran Function Calls from R
interactiveDisplayBase-1.26.3 Base package for enabling powerful shiny web displays of Bioconductor objects
interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
inum-1.0-1 Interval and Enum-Type Representation of Vectors
ipred-0.9-9 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-0.2.2 Generate Isolines and Isobands from Regularly Spaced Elevation Grids
iterators-1.0.12 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-2.7-1 Multilevel Joint Modelling Multiple Imputation
jpeg-0.1-8.1 Read and write JPEG images
jsonlite-1.7.0 A Robust, High Performance JSON Parser and Generator for R
kedd-1.0.3 Kernel Estimator and Bandwidth Selection for Density and Its Derivatives
kernlab-0.9-29 Kernel-Based Machine Learning Lab
kin.cohort-0.7 Analysis of Kin-Cohort Studies
kinship2-1.8.5 Pedigree Functions
klaR-0.6-15 Classification and Visualization
knitr-1.29 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-1.11.7 Kernel Smoothing
kyotil-2019.11-22 Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
labdsv-2.0-1 Ordination and Multivariate Analysis for Ecology
labeling-0.3 Axis Labeling
labelled-2.5.0 Manipulating Labelled Data
laeken-0.5.1 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
lasso2-1.2-20 L1 Constrained Estimation aka `lasso’
latentnet-2.10.5 Latent Position and Cluster Models for Statistical Networks
later-1.1.0.1 Utilities for Scheduling Functions to Execute Later with Event Loops
lattice-0.20-41 Trellis Graphics for R
latticeExtra-0.6-29 Extra Graphical Utilities Based on Lattice
lava-1.6.7 Latent Variable Models
lavaan-0.6-6 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-0.3.3 R Implementation of Leiden Clustering Algorithm
lhs-1.0.2 Latin Hypercube Samples
libcoin-1.0-5 Linear Test Statistics for Permutation Inference
lifecycle-0.2.0 Manage the Life Cycle of your Package Functions
limSolve-1.5.6 Solving Linear Inverse Models
limma-3.44.3 Linear Models for Microarray Data
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
lme4-1.1-23 Linear Mixed-Effects Models using ‘Eigen’ and S4
lmerTest-3.1-2 Tests in Linear Mixed Effects Models
lmtest-0.9-37 Testing Linear Regression Models
locfdr-1.1-8 Computes Local False Discovery Rates
locfit-1.5-9.4 Local Regression, Likelihood and Density Estimation
logcondens-2.1.5 Estimate a Log-Concave Probability Density from Iid Observations
logistf-1.23 Firth’s Bias-Reduced Logistic Regression
logspline-2.1.16 Routines for Logspline Density Estimation
lokern-1.1-8 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-2.2.0 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
lpridge-1.0-8 Local Polynomial (Ridge) Regression
lpsymphony-1.16.0 Symphony integer linear programming solver in R
lqa-1.0-3 Penalized Likelihood Inference for GLMs
lsei-1.2-0.1 Solving Least Squares or Quadratic Programming Problems under Equality/Inequality Constraints
lubridate-1.7.9 Make Dealing with Dates a Little Easier
lumi-2.40.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
mRMRe-2.1.0 “Parallelized Minimum Redundancy, Maximum Relevance (mRMR) Ensemble Feature Selection”
maSigPro-1.60.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
magic-1.5-9 Create and Investigate Magic Squares
magick-2.4.0 Advanced Graphics and Image-Processing in R
magrittr-1.5 A Forward-Pipe Operator for R
manipulateWidget-0.10.1 Add Even More Interactivity to Interactive Charts
mapdata-2.3.0 Extra Map Databases
mapproj-1.2.7 Map Projections
maps-3.3.0 Draw Geographical Maps
maptools-1.0-1 Tools for Handling Spatial Objects
markdown-1.1 Render Markdown with the C Library ‘Sundown’
marray-1.66.0 Exploratory analysis for two-color spotted microarray data
matrixStats-0.56.0 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
matrixcalc-1.0-3 Collection of functions for matrix calculations
maxLik-1.3-8 Maximum Likelihood Estimation and Related Tools
mboost-2.9-2 Model-Based Boosting
mclust-5.4.6 Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
mcmc-0.9-7 Markov Chain Monte Carlo
medflex-0.6-6 Flexible Mediation Analysis Using Natural Effect Models
mediation-4.5.0 Causal Mediation Analysis
memoise-1.1.0 Memoisation of Functions
memuse-4.1-0 Memory Estimation Utilities
metagenomeSeq-1.30.0 Statistical analysis for sparse high-throughput sequencing
methods built in
methylumi-2.34.0 Handle Illumina methylation data
mets-1.2.7.1 Analysis of Multivariate Event Times
mgcv-1.8-31 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
mi-1.0 Missing Data Imputation and Model Checking
mice-3.9.0 Multivariate Imputation by Chained Equations
mime-0.9 Map Filenames to MIME Types
minfi-1.34.0 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<U+000a>approximation
misc3d-0.8-4 Miscellaneous 3D Plots
miscTools-0.6-26 Miscellaneous Tools and Utilities
missForest-1.4 Nonparametric Missing Value Imputation using Random Forest
mitml-0.3-7 Tools for Multiple Imputation in Multilevel Modeling
mitools-2.4 Tools for Multiple Imputation of Missing Data
mixOmics-6.12.1 Omics Data Integration Project
mixtools-1.2.0 Tools for Analyzing Finite Mixture Models
mlbench-2.1-1 Machine Learning Benchmark Problems
mlegp-3.1.7 Maximum Likelihood Estimates of Gaussian Processes
mlogit-1.1-0 Multinomial Logit Models
mlr-2.17.1 Machine Learning in R
mltools-0.3.5 Machine Learning Tools
mnormt-2.0.1 The Multivariate Normal and t Distributions, and Their Truncated Versions
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-0.10.01.02 Keep track of dates in terms of months
mpath-0.3-26 Regularized Linear Models
msa-1.20.0 Multiple Sequence Alignment
msm-1.6.8 Multi-State Markov and Hidden Markov Models in Continuous Time
multcomp-1.4-13 Simultaneous Inference in General Parametric Models
multicool-0.1-11 Permutations of Multisets in Cool-Lex Order
multtest-2.44.0 Resampling-based multiple hypothesis testing
munsell-0.5.0 Utilities for Using Munsell Colours
mvabund-4.1.3 Statistical Methods for Analysing Multivariate Abundance Data
mvnfast-0.2.5 Fast Multivariate Normal and Student’s t Methods
mvtnorm-1.1-1 Multivariate Normal and t Distributions
natserv-1.0.0 ‘NatureServe’ Interface
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-2.34.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
ndtv-0.13.0 Network Dynamic Temporal Visualizations
network-1.16.0 Classes for Relational Data
networkDynamic-0.10.1 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
nleqslv-3.3.2 Solve Systems of Nonlinear Equations
nlme-3.1-148 Linear and Nonlinear Mixed Effects Models
nloptr-1.2.2.1 R Interface to NLopt
nnet-7.3-14 Feed-Forward Neural Networks and Multinomial Log-Linear Models
nnls-1.4 The Lawson-Hanson algorithm for non-negative least squares<U+000a>(NNLS)
nor1mix-1.3-0 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods)
np-0.60-10 Nonparametric Kernel Smoothing Methods for Mixed Data Types
npsurv-0.4-0.1 Nonparametric Survival Analysis
numDeriv-2016.8-1.1 Accurate Numerical Derivatives
numbers-0.7-5 Number-Theoretic Functions
nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
oce-1.2-0 Analysis of Oceanographic Data
oddsratio-2.0.1 Odds Ratio Calculation for GAM(M)s & GLM(M)s
oligoClasses-1.50.0 Classes for high-throughput arrays supported by oligo and crlmm
openCyto-2.0.0 Hierarchical Gating Pipeline for flow cytometry data
openssl-1.4.2 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
openxlsx-4.1.5 Read, Write and Edit xlsx Files
optmatch-0.9-13 Functions for Optimal Matching
optparse-1.6.6 Command Line Option Parser
ordinal-2019.12-10 Regression Models for Ordinal Data
org.Hs.eg.db-3.11.4 Genome wide annotation for Human
pROC-1.16.2 Display and Analyze ROC Curves
pack-0.1-1 Convert values to/from raw vectors
packrat-0.5.0 A Dependency Management System for Projects and their R Package Dependencies
pan-1.6 Multiple Imputation for Multivariate Panel or Clustered Data
parallelMap-1.5.0 Unified Interface to Parallelization Back-Ends
parsedate-1.2.0 Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats
parsnip-0.1.1 A Common API to Modeling and Analysis Functions
partools-1.1.6 Tools for the ‘Parallel’ Package
party-1.3-5 A Laboratory for Recursive Partytioning
partykit-1.2-8 A Toolkit for Recursive Partytioning
pastecs-1.3.21 Package for Analysis of Space-Time Ecological Series
patchwork-1.0.1 The Composer of Plots
pbapply-1.4-2 Adding Progress Bar to ‘*apply’ Functions
pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
pbkrtest-0.4-8.6 Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison
pbs-1.1 Periodic B Splines
pcaMethods-1.80.0 A collection of PCA methods
pcaPP-1.9-73 Robust PCA by Projection Pursuit
pdftools-2.3.1 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-1.1-7.1 Parallelised Estimation of Prediction Error
perm-1.0-0.0 Exact or Asymptotic permutation tests
permute-0.9-5 Functions for Generating Restricted Permutations of Data
phangorn-2.5.5 Phylogenetic Reconstruction and Analysis
pheatmap-1.0.12 Pretty Heatmaps
phylobase-0.8.10 Base Package for Phylogenetic Structures and Comparative Data
phytools-0.7-47 Phylogenetic Tools for Comparative Biology (and Other Things)
pillar-1.4.4 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-0.4-11 Bitmap Images (``Pixel Maps’’)
pkgbuild-1.0.8 Find Tools Needed to Build R Packages
pkgconfig-2.0.3 Private Configuration for ‘R’ Packages
pkgload-1.1.0 Simulate Package Installation and Attach
pkgmaker-0.31.1 Development Utilities for R Packages
plogr-0.2.0 The ‘plog’ C++ Logging Library
plot3D-1.3 Plotting Multi-Dimensional Data
plot3Drgl-1.0.1 Plotting Multi-Dimensional Data - Using ‘rgl’
plotly-4.9.2.1 Create Interactive Web Graphics via ‘plotly.js’
plotrix-3.7-8 Various Plotting Functions
pls-2.7-2 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
polspline-1.1.19 Polynomial Spline Routines
polyclip-1.10-0 Polygon Clipping
polyester-1.24.0 Simulate RNA-seq reads
polynom-1.4-0 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
prabclus-2.3-2 Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data
pracma-2.2.9 Practical Numerical Math Functions
praise-1.0.0 Praise Users
preprocessCore-1.50.0 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-3.4.2 Execute and Control System Processes
prodlim-2019.11.13 Product-Limit Estimation for Censored Event History Analysis
profileModel-0.6.0 Profiling Inference Functions for Various Model Classes
progress-1.2.2 Terminal Progress Bars
promises-1.1.1 Abstractions for Promise-Based Asynchronous Programming
proto-1.0.0 Prototype Object-Based Programming
proxy-0.4-24 Distance and Similarity Measures
pryr-0.1.4 Tools for Computing on the Language
ps-1.3.3 List, Query, Manipulate System Processes
pscl-1.5.5 Political Science Computational Laboratory
pspline-1.0-18 Penalized Smoothing Splines
psych-1.9.12.31 Procedures for Psychological, Psychometric, and Personality Research
psychotools-0.5-1 Psychometric Modeling Infrastructure
pulsar-0.3.6 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
qgam-1.3.2 Smooth Additive Quantile Regression Models
qgraph-1.6.5 Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
qpdf-1.1 Split, Combine and Compress PDF Files
qrnn-2.0.5 Quantile Regression Neural Network
qtl-1.46-2 Tools for Analyzing QTL Experiments
quadprog-1.5-8 Functions to Solve Quadratic Programming Problems
quantmod-0.4.17 Quantitative Financial Modelling Framework
quantreg-5.55 Quantile Regression
quantsmooth-1.54.0 Quantile smoothing and genomic visualization of array data
questionr-0.7.1 Functions to Make Surveys Processing Easier
qvalue-2.20.0 Q-value estimation for false discovery rate control
qvcalc-1.0.2 Quasi Variances for Factor Effects in Statistical Models
r2d3-0.2.3 Interface to ‘D3’ Visualizations
rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
rGADEM-2.36.0 de novo motif discovery
rJava-0.9-12 Low-Level R to Java Interface
randomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and Regression
randomForestSRC-2.9.3 Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
ranger-0.12.1 A Fast Implementation of Random Forests
rappdirs-0.3.1 Application Directories: Determine Where to Save Data, Caches, and Logs
raster-3.3-7 Geographic Data Analysis and Modeling
rasterVis-0.48 Visualization Methods for Raster Data
rbenchmark-1.0.0 Benchmarking routine for R
rcmdcheck-1.3.3 Run ‘R CMD check’ from ‘R’ and Capture Results
rda-1.0.2-2.1 Shrunken Centroids Regularized Discriminant Analysis
readbitmap-0.1.5 Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF)
readr-1.3.1 Read Rectangular Text Data
readxl-1.3.1 Read Excel Files
recipes-0.1.13 Preprocessing Tools to Create Design Matrices
refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from ‘Ensembl’ and ‘UCSC’ Genome Browsers
refund-0.1-21 Regression with Functional Data
regioneR-1.20.1 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
regtools-1.1.0 Regression and Classification Tools
relations-0.6-9 Data Structures and Algorithms for Relations
relevent-1.0-4 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-2.1.1 R Package Installation from Remote Repositories, Including ‘GitHub’
rentrez-1.2.2 ‘Entrez’ in R
repr-1.1.0 Serializable Representations
reprex-0.3.0 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
reticulate-1.16 Interface to ‘Python’
rex-1.2.0 Friendly Regular Expressions
rgenoud-5.8-3.0 R Version of GENetic Optimization Using Derivatives
rgexf-0.16.0 Build, Import and Export GEXF Graph Files
rgl-0.100.54 3D Visualization Using OpenGL
rhdf5-2.32.1 R Interface to HDF5
rio-0.5.16 A Swiss-Army Knife for Data I/O
ritis-0.9.0 Integrated Taxonomic Information System Client
rjags-4-10 Bayesian Graphical Models using MCMC
rjson-0.2.20 JSON for R
rlang-0.4.6 Functions for Base Types and Core R and ‘Tidyverse’ Features
rlecuyer-0.3-5 R Interface to RNG with Multiple Streams
rmarkdown-2.3 Dynamic Documents for R
rmeta-3.0 Meta-Analysis
rms-6.0-0 Regression Modeling Strategies
rncl-0.8.4 An Interface to the Nexus Class Library
rngtools-1.5 Utility Functions for Working with Random Number Generators
robustbase-0.93-6 Basic Robust Statistics
rootSolve-1.8.2.1 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
rotl-3.0.10 Interface to the ‘Open Tree of Life’ API
roxygen2-7.1.1 In-Line Documentation for R
rpart-4.1-15 Recursive Partitioning and Regression Trees
rprojroot-1.3-2 Finding Files in Project Subdirectories
rrcov-1.5-2 Scalable Robust Estimators with High Breakdown Point
rredlist-0.6.0 ‘IUCN’ Red List Client
rsample-0.0.7 General Resampling Infrastructure
rsconnect-0.8.16 Deployment Interface for R Markdown Documents and Shiny Applications
rslurm-0.5.0 Submit R Calculations to a ‘Slurm’ Cluster
rstan-2.19.3 R Interface to Stan
rstanarm-2.19.3 Bayesian Applied Regression Modeling via Stan
rstantools-2.1.0 Tools for Developing R Packages Interfacing with ‘Stan’
rstudioapi-0.11 Safely Access the RStudio API
rsvd-1.0.3 Randomized Singular Value Decomposition
rsvg-2.1 Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
rtracklayer-1.48.0 R interface to genome annotation files and the UCSC genome browser
rvcheck-0.1.8 R/Package Version Check
rversions-2.0.2 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
rvest-0.3.5 Easily Harvest (Scrape) Web Pages
rzmq-0.9.7 R Bindings for ‘ZeroMQ’
sampling-2.8 Survey Sampling
samr-3.0 SAM: Significance Analysis of Microarrays
sandwich-2.5-1 Robust Covariance Matrix Estimators
scales-1.1.1 Scale Functions for Visualization
scatterplot3d-0.3-41 3D Scatter Plot
scidb-2.0.0 An R Interface to SciDB
scrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
sctransform-0.2.1 Variance Stabilizing Transformations for Single Cell UMI Data
seewave-2.1.6 Sound Analysis and Synthesis
segmented-1.2-0 Regression Models with Break-Points / Change-Points Estimation
selectr-0.4-2 Translate CSS Selectors to XPath Expressions
sem-3.1-11 Structural Equation Models
sendmailR-1.2-1 send email using R
seqLogo-1.54.3 Sequence logos for DNA sequence alignments
seqinr-3.6-1 Biological Sequences Retrieval and Analysis
servr-0.17 A Simple HTTP Server to Serve Static Files or Dynamic Documents
sessioninfo-1.1.1 R Session Information
sets-1.0-18 Sets, Generalized Sets, Customizable Sets and Intervals
sfsmisc-1.1-7 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
shape-1.4.4 Functions for Plotting Graphical Shapes, Colors
shapefiles-0.7 Read and Write ESRI Shapefiles
shiny-1.5.0 Web Application Framework for R
shinyBS-0.61 Twitter Bootstrap Components for Shiny
shinyFiles-0.8.0 A Server-Side File System Viewer for Shiny
shinycssloaders-0.3 Add CSS Loading Animations to ‘shiny’ Outputs
shinydashboard-0.7.1 Create Dashboards with ‘Shiny’
shinyjs-1.1 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-1.1.2 Themes for Shiny
sigaR-1.35.0 Statistics for Integrative Genomics Analyses in R
siggenes-1.62.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
signal-0.7-6 Signal Processing
sitmo-2.0.1 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header Files
slam-0.1-47 Sparse Lightweight Arrays and Matrices
sm-2.2-5.6 Smoothing Methods for Nonparametric Regression and Density Estimation
smoother-1.1 Functions Relating to the Smoothing of Numerical Data
sn-1.6-2 The Skew-Normal and Related Distributions Such as the Skew-t
sna-2.5 Tools for Social Network Analysis
snow-0.4-3 Simple Network of Workstations
snowfall-1.84-6.1 Easier cluster computing (based on snow).
snpStats-1.38.0 SnpMatrix and XSnpMatrix classes and methods
solrium-1.1.4 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-1.4-2 Classes and Methods for Spatial Data
spData-0.3.5 Datasets for Spatial Analysis
spaMM-3.3.0 Mixed-Effect Models, Particularly Spatial Models
spam-2.5-1 SPArse Matrix
sparklyr-1.3.0 R Interface to Apache Spark
spatial-7.3-12 Functions for Kriging and Point Pattern Analysis
spatstat-1.64-1 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
spatstat.data-1.4-3 Datasets for ‘spatstat’
spatstat.utils-1.17-0 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
sqldf-0.4-11 Manipulate R Data Frames Using SQL
ssgraph-1.12 Bayesian Graphical Estimation using Spike-and-Slab Priors
stabledist-0.7-1 Stable Distribution Functions
stabs-0.6-3 Stability Selection with Error Control
startupmsg-0.9.6 Utilities for Start-Up Messages
statmod-1.4.34 Statistical Modeling
statnet-2019.6 Software Tools for the Statistical Analysis of Network Data
statnet.common-4.3.0 Common R Scripts and Utilities Used by the Statnet Project Software
stats built in
stats4 built in
stopwords-2.0 Multilingual Stopword Lists
stringdist-0.9.5.5 Approximate String Matching and String Distance Functions
stringi-1.4.6 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-1.3.2 Non-Invasive Pretty Printing of R Code
subplex-1.6 Unconstrained Optimization using the Subplex Algorithm
survey-4.0 Analysis of Complex Survey Samples
survival-3.2-3 Survival Analysis
survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
svd-0.5 Interfaces to Various State-of-Art SVD and Eigensolvers
sys-3.3 Powerful and Reliable Tools for Running System Commands in R
systemPipeR-1.22.0 systemPipeR: NGS workflow and report generation environment
tables-0.9.3 Formula-Driven Table Generation
taxize-0.9.97 Taxonomic Information from Around the Web
tclust-1.4-1 Robust Trimmed Clustering
tensor-1.5 Tensor product of arrays
tensorA-0.36.1 Advanced Tensor Arithmetic with Named Indices
tergm-3.6.1 Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
testthat-2.3.2 Unit Testing for R
threejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globes
tibble-3.0.1 Simple Data Frames
tictoc-1.0 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-0.1.0 Easily Install and Load the ‘Tidymodels’ Packages
tidyposterior-0.0.3 Bayesian Analysis to Compare Models using Resampling Statistics
tidypredict-0.4.5 Run Predictions Inside the Database
tidyr-1.1.0 Tidy Messy Data
tidyselect-1.1.0 Select from a Set of Strings
tidytext-0.2.4 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Tools
tidytree-0.3.3 A Tidy Tool for Phylogenetic Tree Data Manipulation
tidyverse-1.3.0 Easily Install and Load the ‘Tidyverse’
tiff-0.1-5 Read and write TIFF images
tilingArray-1.66.0 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-1.9.5 Flexible Regression Models for Survival Data
tinytex-0.24 Helper Functions to Install and Maintain ‘TeX Live’, and Compile ‘LaTeX’ Documents
tkWidgets-1.66.0 R based tk widgets
tkrplot-0.0-24 TK Rplot
tm-0.7-7 Text Mining Package
tmle-1.5.0-1 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-0.2-11 Topic Models
tree-1.0-40 Classification and Regression Trees
treeio-1.12.0 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-0.10-47 Time Series Analysis and Computational Finance
tseriesChaos-0.1-13.1 Analysis of Nonlinear Time Series
tsna-0.3.1 Tools for Temporal Social Network Analysis
tsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
tune-0.1.0 Tidy Tuning Tools
tuneR-1.3.3 Analysis of Music and Speech
tweedie-2.3.2 Evaluation of Tweedie Exponential Family Models
tweenr-1.0.1 Interpolate Data for Smooth Animations
ucminf-1.1-4 General-Purpose Unconstrained Non-Linear Optimization
udunits2-0.13 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-0.6-7 Measurement Units for R Vectors
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-2.1-0 Unit Root Tests for Seasonal Time Series
usethis-1.6.1 Automate Package and Project Setup
utf8-1.1.4 Unicode Text Processing
utils built in
uuid-0.1-4 Tools for Generating and Handling of UUIDs
uwot-0.1.8 The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
vcd-1.4-7 Visualizing Categorical Data
vcfR-1.11.0 Manipulate and Visualize VCF Data
vctrs-0.3.1 Vector Helpers
vegan-2.5-6 Community Ecology Package
venn-1.9 Draw Venn Diagrams
vimp-2.1.0 Perform Inference on Algorithm-Agnostic Variable Importance
vioplot-0.3.5 Violin Plot
vipor-0.4.5 Plot Categorical Data Using Quasirandom Noise and Density Estimates
viridis-0.5.1 Default Color Maps from ‘matplotlib’
viridisLite-0.3.0 Default Color Maps from ‘matplotlib’ (Lite Version)
visNetwork-2.0.9 Network Visualization using ‘vis.js’ Library
vsn-3.56.0 Variance stabilization and calibration for microarray data
waveslim-1.8.2 Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing
wavethresh-4.6.8 Wavelets Statistics and Transforms
webp-1.0 A New Format for Lossless and Lossy Image Compression
webshot-0.5.2 Take Screenshots of Web Pages
whisker-0.4 for R, Logicless Templating
widgetTools-1.66.0 Creates an interactive tcltk widget
wikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’
withr-2.2.0 Run Code ‘With’ Temporarily Modified Global State
workflows-0.1.1 Modeling Workflows
worrms-0.4.0 World Register of Marine Species (WoRMS) Client
xCell 1.2
xfun-0.15 Miscellaneous Functions by ‘Yihui Xie’
xgboost-1.1.1.1 Extreme Gradient Boosting
xlsx-0.6.3 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-1.0.3 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-0.12-0 eXtensible Time Series
yaml-2.2.1 Methods to Convert R Data to YAML and Back
yardstick-0.0.6 Tidy Characterizations of Model Performance
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-2.0.4 Cross-Platform ‘zip’ Compression
zlibbioc-1.34.0 An R packaged zlib-1.2.5
zoo-1.8-8 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)