Package List
- ADGofTest-0.3 Anderson-Darling GoF test
- ALDEx2 1.10.0
- AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.
- AgiMicroRna 2.28.0
- AlgDesign-1.1-7.3 Algorithmic Experimental Design
- AnnotationDbi 1.40.0
- AnnotationFilter 1.2.0
- AnnotationForge 1.20.0
- AnnotationHub 2.10.0
- BB-2014.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
- BBmisc-1.11 Miscellaneous Helper Functions for B. Bischl
- BDgraph-2.42 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
- BH-1.65.0-1 Boost C++ Header Files
- BSgenome 1.46.0
- BSgenome.Hsapiens.UCSC.hg19 1.4.0
- BatchJobs-1.6 Batch Computing with R
- Bhat-0.9-10 General likelihood exploration
- BiasedUrn-1.07 Biased Urn Model Distributions
- Biobase 2.38.0
- BiocGenerics 0.24.0
- BiocInstaller 1.28.0
- BiocParallel 1.12.0
- Biostrings 2.46.0
- BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
- Bolstad-0.2-34 Functions for Elementary Bayesian Inference
- Bolstad2-1.0-28 Bolstad functions
- BradleyTerry2-1.0-8 Bradley-Terry Models
- Brobdingnag-1.2-4 Very Large Numbers in R
- CGEN 3.14.0
- CGHbase 1.38.0
- CVST-0.2-1 Fast Cross-Validation via Sequential Testing
- Cairo-1.5-9 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 2.44.0
- CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
- DAAG-1.22 Data Analysis and Graphics Data and Functions
- DBI-0.7 R Database Interface
- DEGseq 1.32.0
- DESeq2 1.18.0
- DEoptimR-1.0-8 Differential Evolution Optimization in Pure R
- DNAcopy 1.52.0
- DRR-0.0.2 Dimensionality Reduction via Regression
- DT-0.2 A Wrapper of the JavaScript Library ‘DataTables’
- DelayedArray 0.4.1
- Deriv-3.8.2 Symbolic Differentiation
- DiagrammeR-0.9.2 Graph/Network Visualization
- DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
- DynDoc 1.56.0
- EBImage 4.20.0
- EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
- EpiModel-1.5.0 Mathematical Modeling of Infectious Disease Dynamics
- FDb.InfiniumMethylation.hg19 2.2.0
- FNN-1.1 Fast Nearest Neighbor Search Algorithms and Applications
- FactoMineR-1.38 Multivariate Exploratory Data Analysis and Data Mining
- Formula-1.2-2 Extended Model Formulas
- GENESIS 2.8.0
- GEOquery 2.46.0
- GGally-1.3.2 Extension to ‘ggplot2’
- GO.db 3.4.2
- GOstats 2.44.0
- GSA-1.03 Gene set analysis
- GSEABase 1.40.0
- GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
- GWASTools 1.24.0
- GeneNet-1.2.13 Modeling and Inferring Gene Networks
- GenomeGraphs 1.38.0
- GenomeInfoDb 1.14.0
- GenomeInfoDbData 0.99.1
- GenomicAlignments 1.14.0
- GenomicFeatures 1.30.0
- GenomicFiles 1.14.0
- GenomicRanges 1.30.0
- Gviz 1.22.0
- HCsnip 1.17.0
- HMMcopy 1.20.0
- HaploSim-1.8.4 Functions to simulate haplotypes
- Hmisc-4.0-3 Harrell Miscellaneous
- Homo.sapiens 1.3.1
- IDPmisc-1.1.17 Utilities of Institute of Data Analyses and Process Design<U+000a>(www.idp.zhaw.ch)
- IRanges 2.12.0
- IRdisplay-0.4.4 ‘Jupyter’ Display Machinery
- IlluminaHumanMethylation450kmanifest 0.4.0
- Iso-0.0-17 Functions to Perform Isotonic Regression
- KEGG.db 3.2.3
- KEGGREST 1.18.0
- KEGGgraph 1.38.0
- KEGGprofile 1.20.0
- KernSmooth-2.23-15 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
- LearnBayes-2.15 Functions for Learning Bayesian Inference
- Lmoments-1.2-3 L-Moments and Quantile Mixtures
- LogicReg-1.5.9 Logic Regression
- MASS-7.3-47 Support Functions and Datasets for Venables and Ripley’s MASS
- MCMCglmm-2.25 MCMC Generalised Linear Mixed Models
- MPV-1.38 Data Sets from Montgomery, Peck and Vining
- Matrix-1.2-11 Sparse and Dense Matrix Classes and Methods
- MatrixModels-0.4-1 Modelling with Sparse And Dense Matrices
- Mfuzz 2.38.0
- ModelMetrics-1.1.0 Rapid Calculation of Model Metrics
- MotIV 1.34.0
- NLP-0.1-11 Natural Language Processing Infrastructure
- NMF-0.20.6 Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)
- NOISeq 2.22.0
- OrganismDbi 1.20.0
- PBSddesolve-1.12.2 Solver for Delay Differential Equations
- PFAM.db 3.4.2
- PICS 2.22.0
- ParamHelpers-1.10 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
- PolynomF-0.94 Polynomials in R
- ProtGenerics 1.10.0
- R.matlab-3.6.1 Read and Write MAT Files and Call MATLAB from Within R
- R.methodsS3-1.7.1 S3 Methods Simplified
- R.oo-1.21.0 R Object-Oriented Programming with or without References
- R.utils-2.6.0 Various Programming Utilities
- R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
- R2jags-0.5-7 Using R to Run ‘JAGS’
- R6-2.2.2 Classes with Reference Semantics
- RANN-2.5.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
Metric
- RBGL-1.54.0 An interface to the BOOST graph library
- RCircos-1.2.0 Circos 2D Track Plot
- RColorBrewer-1.1-2 ColorBrewer Palettes
- RCurl-1.95-4.8 General Network (HTTP/FTP/…) Client Interface for R
- REDCapR-0.9.8 Interaction Between R and REDCap
- RGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock Data
- RJSONIO-1.3-0 Serialize R objects to JSON, JavaScript Object Notation
- RMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>Theory
- RMySQL-0.10.13 Database Interface and ‘MySQL’ Driver for R
- RNASeqPower 1.18.0
- RNeXML-2.0.7 Semantically Rich I/O for the ‘NeXML’ Format
- ROCR-1.0-7 Visualizing the Performance of Scoring Classifiers
- RODBC-1.3-15 ODBC Database Access
- RPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database System
- RSNNS-0.4-9 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)
- RSQLite-2.0 ‘SQLite’ Interface for R
- RSclient-0.7-3 Client for Rserve
- RSpectra-0.12-0 Solvers for Large-Scale Eigenvalue and SVD Problems
- RUnit-0.4.31 R Unit Test Framework
- RWeka-0.4-35 R/Weka Interface
- RWekajars-3.9.1-4 R/Weka Interface Jars
- Rcpp-0.12.13 Seamless R and C++ Integration
- RcppArmadillo-0.8.100.1.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra
Library
- RcppEigen-0.3.3.3.0 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra
Library
- RcppParallel-4.3.20 Parallel Programming Tools for ‘Rcpp’
- RcppRoll-0.2.2 Efficient Rolling / Windowed Operations
- ReportingTools 2.17.2
- Rglpk-0.6-3 R/GNU Linear Programming Kit Interface
- Rgraphviz-2.22.0 Provides plotting capabilities for R graph objects
- Rhpc-0.15-244 Permits *apply() Style Dispatch for ‘HPC’
- Ringo 1.42.0
- Rlabkey-2.1.136 Data Exchange Between R and ‘LabKey’ Server
- Rmpi-0.6-6 Interface (Wrapper) to MPI (Message-Passing Interface)
- Rook-1.1-1 Rook - a web server interface for R
- Rsamtools 1.30.0
- Rsubread 1.28.0
- Rttf2pt1-1.3.4 ‘ttf2pt1’ Program
- S4Vectors 0.16.0
- SNPRelate-1.12.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
- SPIA 2.30.0
- SeqArray 1.18.1
- SeqVarTools 1.16.0
- ShortRead 1.36.0
- SparseM-1.77 Sparse Linear Algebra
- StanHeaders-2.16.0-1 C++ Header Files for Stan
- SummarizedExperiment 1.8.0
- SuperLearner-2.0-22 Super Learner Prediction
- SuppDists-1.1-9.4 Supplementary Distributions
- TH.data-1.0-8 TH’s Data Archive
- TTR-0.23-2 Technical Trading Rules
- TeachingDemos-2.10 Demonstrations for Teaching and Learning
- TitanCNA 1.16.0
- TraMineR-2.0-7 Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
- TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
- VGAM-1.0-4 Vector Generalized Linear and Additive Models
- VariantAnnotation 1.24.0
- VennDiagram-1.6.17 Generate High-Resolution Venn and Euler Plots
- WikidataR-1.4.0 API Client Library for ‘Wikidata’
- WikipediR-1.5.0 A MediaWiki API Wrapper
- XML-3.98-1.9 Tools for Parsing and Generating XML Within R and S-Plus
- XVector 0.18.0
- abc-2.1 Tools for Approximate Bayesian Computation (ABC)
- abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)
- abind-1.4-5 Combine Multidimensional Arrays
- acepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformations
- adabag-4.1 Applies Multiclass AdaBoost.M1, SAMME and Bagging
- ade4-1.7-8 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
- adegenet-2.1.0 Exploratory Analysis of Genetic and Genomic Data
- adephylo-1.1-10 Exploratory Analyses for the Phylogenetic Comparative Method
- affy 1.56.0
- affycoretools 1.50.0
- affyio 1.48.0
- akima-0.6-2 Interpolation of Irregularly and Regularly Spaced Data
- alr3-2.0.5 Data to Accompany Applied Linear Regression 3rd Edition
- animation-2.5 A Gallery of Animations in Statistics and Utilities to Create
Animations
- annaffy 1.50.0
- annotate 1.56.0
- ape-5.0 Analyses of Phylogenetics and Evolution
- argparser-0.4 Command-Line Argument Parser
- arm-1.9-3 Data Analysis Using Regression and Multilevel/Hierarchical
Models
- ascat 2.5
- assertthat-0.2.0 Easy Pre and Post Assertions
- backports-1.1.1 Reimplementations of Functions Introduced Since R-3.0.0
- base built in
- base64-2.0 Base64 Encoder and Decoder
- base64enc-0.1-3 Tools for base64 encoding
- baySeq 2.12.0
- bdsmatrix-1.3-2 Routines for Block Diagonal Symmetric Matrices
- beanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)
- benchmark-0.3-6 Benchmark Experiments Toolbox
- biglm-0.9-1 bounded memory linear and generalized linear models
- bigmemory-4.5.19 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 Parametrized Active Bindings
- bindrcpp-0.2 An ‘Rcpp’ Interface to Active Bindings
- bio3d-2.3-3 Biological Structure Analysis
- biom-0.3.12 An interface package (beta) for the BIOM file format.
- biomaRt 2.34.0
- biomformat 1.6.0
- biovizBase 1.26.0
- bit-1.1-12 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-1.1.0 A Simple S3 Class for Representing Vectors of Binary Data
(‘BLOBS’)
- bnlearn-4.2 Bayesian Network Structure Learning, Parameter Learning and
Inference
- bold-0.5.0 Interface to Bold Systems API
- boot-1.3-20 Bootstrap Functions (Originally by Angelo Canty for S)
- bootstrap-2017.2 Functions for the Book “An Introduction to the Bootstrap”
- brew-1.0-6 Templating Framework for Report Generation
- brglm-0.6.1 Bias Reduction in Binomial-Response Generalized Linear Models
- broom-0.4.2 Convert Statistical Analysis Objects into Tidy Data Frames
- bumphunter 1.20.0
- caTools-1.17.1 Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
- calibrate-1.7.2 Calibration of Scatterplot and Biplot Axes
- car-2.1-5 Companion to Applied Regression
- caret-6.0-77 Classification and Regression Training
- catdata-1.2.1 Categorical Data
- cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
- cgdsr-1.2.6 R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
- checkmate-1.8.5 Fast and Versatile Argument Checks
- chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
- chipseq 1.28.0
- chron-2.3-51 Chronological Objects which can Handle Dates and Times
- clValid-0.6-6 Validation of Clustering Results
- class-7.3-14 Functions for Classification
- cluster-2.0.6 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et
al.
- clusterGeneration-1.3.4 Random Cluster Generation (with Specified Degree of Separation)
- clusterRepro-0.5-1.1 Reproducibility of gene expression clusters
- coda-0.19-1 Output Analysis and Diagnostics for MCMC
- codetools-0.2-15 Code Analysis Tools for R
- coin-1.2-1 Conditional Inference Procedures in a Permutation Test Framework
- colorspace-1.3-2 Color Space Manipulation
- combinat-0.0-8 combinatorics utilities
- commonmark-1.4 High Performance CommonMark and Github Markdown Rendering in R
- compare-0.2-6 Comparing Objects for Differences
- compiler built in
- config-0.2 Manage Environment Specific Configuration Values
- copula-0.999-18 Multivariate Dependence with Copulas
- corpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlation
- coxme-2.2-5 Mixed Effects Cox Models
- crayon-1.3.4 Colored Terminal Output
- crosstalk-1.0.0 Inter-Widget Interactivity for HTML Widgets
- crul-0.4.0 HTTP Client
- cubature-1.3-11 Adaptive Multivariate Integration over Hypercubes
- cummeRbund 2.20.0
- curl-3.0 A Modern and Flexible Web Client for R
- cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
- d3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from R
- dada2 1.6.0
- data.table-1.10.4-3 Extension of
data.frame
- datasets built in
- dbplyr-1.1.0 A ‘dplyr’ Back End for Databases
- ddalpha-1.3.1 Depth-Based Classification and Calculation of Data Depth
- deSolve-1.20 Solvers for Initial Value Problems of Differential Equations
(‘ODE’, ‘DAE’, ‘DDE’)
- deal-1.2-37 Learning Bayesian Networks with Mixed Variables
- degreenet-1.3-1 Models for Skewed Count Distributions Relevant to Networks
- deldir-0.1-14 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
- derfinder 1.12.0
- derfinderHelper 1.12.0
- desc-1.1.1 Manipulate DESCRIPTION Files
- devtools-1.13.3 Tools to Make Developing R Packages Easier
- dfoptim-2016.7-1 Derivative-Free Optimization
- diamonds-1.0-5 Analysis and sampling grids from diamond partitions
- dichromat-2.0-0 Color Schemes for Dichromats
- digest-0.6.12 Create Compact Hash Digests of R Objects
- dimRed-0.1.0 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-1.0-4 Method Functions for Confidence Intervals and to Distill
Information from an Object
- diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis
Package
- doAzureParallel 0.5.0
- doMC-1.3.4 Foreach Parallel Adaptor for ‘parallel’
- doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
- doParallel-1.0.11 Foreach Parallel Adaptor for the ‘parallel’ Package
- doRNG-1.6.6 Generic Reproducible Parallel Backend for ‘foreach’ Loops
- doSNOW-1.0.15 Foreach Parallel Adaptor for the ‘snow’ Package
- dotCall64-0.9-04 Enhanced Foreign Function Interface Supporting Long Vectors
- downloader-0.4 Download Files over HTTP and HTTPS
- dplyr-0.7.4 A Grammar of Data Manipulation
- dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
- e1071-1.6-8 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
- edgeR 3.20.1
- elasticnet-1.1 Elastic-Net for Sparse Estimation and Sparse PCA
- ellipse-0.3-8 Functions for Drawing Ellipses and Ellipse-Like Confidence
Regions
- ensembldb 2.2.0
- ergm-3.8.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks
- ergm.count-3.2.2 Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
- evaluate-0.10.1 Parsing and Evaluation Tools that Provide More Details than the
Default
- expm-0.999-2 Matrix Exponential, Log, ‘etc’
- expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
- extRemes-2.0-8 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)
- fastICA-1.2-1 FastICA Algorithms to Perform ICA and Projection Pursuit
- fastcluster-1.1.24 Fast Hierarchical Clustering Routines for R and ‘Python’
- fastmatch-1.1-0 Fast match() function
- fastseg 1.24.0
- fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
- fda-2.4.7 Functional Data Analysis
- fdrtool-1.2.15 Estimation of (Local) False Discovery Rates and Higher Criticism
- ff-2.2-13 Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
- ffbase-0.12.3 Basic Statistical Functions for Package ‘ff’
- fftw-1.0-4 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-9.0 Tools for Spatial Data
- filehash-2.4-1 Simple Key-Value Database
- fit.models-0.5-14 Compare Fitted Models
- flashClust-1.01-2 Implementation of optimal hierarchical clustering
- flexclust-1.3-4 Flexible Cluster Algorithms
- flexmix-2.3-14 Flexible Mixture Modeling
- flowCore 1.44.0
- flowViz 1.42.0
- flowWorkspace 3.26.1
- fma-2.3 Data Sets from “Forecasting: Methods and Applications” by
Makridakis, Wheelwright & Hyndman (1998)
- foreach-1.4.3 Provides Foreach Looping Construct for R
- forecast-8.2 Forecasting Functions for Time Series and Linear Models
- foreign-0.8-69 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’,
‘Systat’, ‘Weka’, ‘dBase’, …
- formatR-1.5 Format R Code Automatically
- fossil-0.3.7 Palaeoecological and Palaeogeographical Analysis Tools
- fpc-2.1-10 Flexible Procedures for Clustering
- fpp-0.5 Data for “Forecasting: principles and practice”
- fracdiff-1.4-2 Fractionally differenced ARIMA aka ARFIMA(p,d,q) models
- fts-0.9.9 R interface to tslib (a time series library in c++)
- futile.logger-1.4.3 A Logging Utility for R
- futile.options-1.0.0 Futile Options Management
- gage 2.28.0
- gam-1.14-4 Generalized Additive Models
- gamlss.data-5.0-0 GAMLSS Data
- gamlss.dist-5.0-3 Distributions for Generalized Additive Models for Location Scale
and Shape
- gap-1.1-17 Genetic Analysis Package
- gbm-2.1.3 Generalized Boosted Regression Models
- gclus-1.3.1 Clustering Graphics
- gcrma 2.50.0
- gdata-2.18.0 Various R Programming Tools for Data Manipulation
- gdsfmt-1.14.0 R Interface to CoreArray Genomic Data Structure (GDS) files
- geepack-1.2-1 Generalized Estimating Equation Package
- geiger-2.0.6 Analysis of Evolutionary Diversification
- geneLenDataBase 1.14.0
- genefilter 1.60.0
- geneplotter 1.56.0
- genoset 1.34.0
- geometry-0.3-6 Mesh Generation and Surface Tesselation
- getopt-1.20.0 C-Like ‘getopt’ Behavior
- ggbio 1.26.0
- ggm-2.3 Functions for graphical Markov models
- ggplot2-2.2.1 Create Elegant Data Visualisations Using the Grammar of Graphics
- ggvis-0.4.3 Interactive Grammar of Graphics
- git2r-0.19.0 Provides Access to Git Repositories
- glasso-1.8 Graphical lasso- estimation of Gaussian graphical models
- glmnet-2.0-13 Lasso and Elastic-Net Regularized Generalized Linear Models
- glmpath-0.97 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Model
- glue-1.2.0 Interpreted String Literals
- gmm-1.6-1 Generalized Method of Moments and Generalized Empirical
Likelihood
- gmodels-2.16.2 Various R Programming Tools for Model Fitting
- goftest-1.1-1 Classical Goodness-of-Fit Tests for Univariate Distributions
- goseq 1.30.0
- gower-0.1.2 Gower’s Distance
- gplots-3.0.1 Various R Programming Tools for Plotting Data
- grDevices built in
- graph-1.56.0 graph: A package to handle graph data structures
- graphics built in
- grid built in
- gridBase-0.4-7 Integration of base and grid graphics
- gridExtra-2.3 Miscellaneous Functions for “Grid” Graphics
- gsalib-2.1 Utility Functions For GATK
- gsl-1.9-10.3 Wrapper for the Gnu Scientific Library
- gsubfn-0.6-6 Utilities for Strings and Function Arguments
- gtable-0.2.0 Arrange ‘Grobs’ in Tables
- gtools-3.5.0 Various R Programming Tools
- hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm
- haplo.stats-1.7.7 Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
- hexbin-1.27.1 Hexagonal Binning Routines
- hgu133plus2.db 3.2.3
- highr-0.6 Syntax Highlighting for R Source Code
- hms-0.3 Pretty Time of Day
- hopach-2.38.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
- htmlTable-1.9 Advanced Tables for Markdown/HTML
- htmltools-0.3.6 Tools for HTML
- htmlwidgets-0.9 HTML Widgets for R
- httpcode-0.2.0 ‘HTTP’ Status Code Helper
- httpuv-1.3.5 HTTP and WebSocket Server Library
- httr-1.3.1 Tools for Working with URLs and HTTP
- huge-1.2.7 High-Dimensional Undirected Graph Estimation
- hwriter-1.3.2 HTML Writer - Outputs R objects in HTML format
- idr-1.2 Irreproducible discovery rate
- igraph-1.1.2 Network Analysis and Visualization
- igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
- illuminaio 0.20.0
- impute-1.52.0 impute: Imputation for microarray data
- inferference-0.5.4 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
- inline-0.3.14 Functions to Inline C, C++, Fortran Function Calls from R
- interactiveDisplayBase 1.16.0
- interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
- ipred-0.9-6 Improved Predictors
- irace-2.4 Iterated Racing for Automatic Algorithm Configuration
- irlba-2.3.1 Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
- iterators-1.0.8 Provides Iterator Construct for R
- itertools-0.1-3 Iterator Tools
- its-1.1.8 Irregular Time Series
- jpeg-0.1-8 Read and write JPEG images
- jsonlite-1.5 A Robust, High Performance JSON Parser and Generator for R
- kernlab-0.9-25 Kernel-Based Machine Learning Lab
- kin.cohort-0.7 Analysis of Kin-Cohort Studies
- kinship2-1.6.4 Pedigree Functions
- klaR-0.6-12 Classification and Visualization
- knitr-1.17 A General-Purpose Package for Dynamic Report Generation in R
- kohonen-3.0.4 Supervised and Unsupervised Self-Organising Maps
- ks-1.10.7 Kernel Smoothing
- kyotil-2017.10-31 Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
- labdsv-1.8-0 Ordination and Multivariate Analysis for Ecology
- labeling-0.3 Axis Labeling
- lambda.r-1.2 Modeling Data with Functional Programming
- lars-1.2 Least Angle Regression, Lasso and Forward Stagewise
- lasso2-1.2-19 L1 constrained estimation aka `lasso’
- latentnet-2.8.0 Latent Position and Cluster Models for Statistical Networks
- lattice-0.20-35 Trellis Graphics for R
- latticeExtra-0.6-28 Extra Graphical Utilities Based on Lattice
- lava-1.5.1 Latent Variable Models
- lavaan-0.5-23.1097 Latent Variable Analysis
- lazy-1.2-15 Lazy Learning for Local Regression
- lazyeval-0.2.1 Lazy (Non-Standard) Evaluation
- leaps-3.0 Regression Subset Selection
- lhs-0.14 Latin Hypercube Samples
- limma-3.34.0 Linear Models for Microarray Data
- lintr-1.0.1 A ‘Linter’ for R Code
- lme4-1.1-14 Linear Mixed-Effects Models using ‘Eigen’ and S4
- lmtest-0.9-35 Testing Linear Regression Models
- locfit-1.5-9.1 Local Regression, Likelihood and Density Estimation.
- logcondens-2.1.5 Estimate a Log-Concave Probability Density from Iid Observations
- logistf-1.22 Firth’s Bias-Reduced Logistic Regression
- logspline-2.1.9 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-1.0-0 Statistics for Long-Memory Processes (Jan Beran) – Data and<U+000a>Functions
- lpSolve-5.6.13 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
- lpridge-1.0-7 Local Polynomial (Ridge) Regression
- lubridate-1.7.1 Make Dealing with Dates a Little Easier
- lumi 2.30.0
- maSigPro 1.50.0
- magic-1.5-6 Create and Investigate Magic Squares
- magrittr-1.5 A Forward-Pipe Operator for R
- mapdata-2.2-6 Extra Map Databases
- mapproj-1.2-5 Map Projections
- maps-3.2.0 Draw Geographical Maps
- maptools-0.9-2 Tools for Reading and Handling Spatial Objects
- markdown-0.8 ‘Markdown’ Rendering for R
- marray 1.56.0
- matrixStats-0.52.2 Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
- matrixcalc-1.0-3 Collection of functions for matrix calculations
- maxLik-1.3-4 Maximum Likelihood Estimation and Related Tools
- mboost-2.8-1 Model-Based Boosting
- mclust-5.3 Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
- mediation-4.4.6 Causal Mediation Analysis
- memoise-1.1.0 Memoisation of Functions
- metagenomeSeq 1.20.0
- methods built in
- methylumi 2.24.1
- mets-1.2.2 Analysis of Multivariate Event Times
- mgcv-1.8-22 Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
- mi-1.0 Missing Data Imputation and Model Checking
- mice-2.46.0 Multivariate Imputation by Chained Equations
- mime-0.5 Map Filenames to MIME Types
- minfi 1.24.0
- minqa-1.2.4 Derivative-free optimization algorithms by quadratic<U+000a>approximation
- misc3d-0.8-4 Miscellaneous 3D Plots
- miscTools-0.6-22 Miscellaneous Tools and Utilities
- mixOmics-6.3.0 Omics Data Integration Project
- mixtools-1.1.0 Tools for Analyzing Finite Mixture Models
- mlbench-2.1-1 Machine Learning Benchmark Problems
- mlogit-0.2-4 Multinomial Logit Models
- mlr-2.11 Machine Learning in R
- mnormt-1.5-5 The Multivariate Normal and t Distributions
- modeltools-0.2-21 Tools and Classes for Statistical Models
- mondate-0.10.01.02 Keep track of dates in terms of months
- mongolite-1.2 Fast and Simple ‘MongoDB’ Client for R
- msm-1.6.4 Multi-State Markov and Hidden Markov Models in Continuous Time
- multcomp-1.4-7 Simultaneous Inference in General Parametric Models
- multicool-0.1-10 Permutations of Multisets in Cool-Lex Order
- multtest-2.34.0 Resampling-based multiple hypothesis testing
- munsell-0.4.3 Utilities for Using Munsell Colours
- mvtnorm-1.0-6 Multivariate Normal and t Distributions
- natserv-0.1.4 ‘NatureServe’ Interface
- ncbit-2013.03.29 retrieve and build NBCI taxonomic data
- ncdf4-1.16 Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
- ncdfFlow 2.24.0
- ndtv-0.10.0 Network Dynamic Temporal Visualizations
- network-1.13.0 Classes for Relational Data
- networkDynamic-0.9.0 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
- nleqslv-3.3.1 Solve Systems of Nonlinear Equations
- nlme-3.1-131 Linear and Nonlinear Mixed Effects Models
- nloptr-1.0.4 R interface to NLopt
- nnet-7.3-12 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-1.2-3 Normal (1-d) Mixture Models (S3 Classes and Methods)
- np-0.60-3 Nonparametric Kernel Smoothing Methods for Mixed Data Types
- numDeriv-2016.8-1 Accurate Numerical Derivatives
- nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
- oligoClasses 1.40.0
- openssl-0.9.8 Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
- openxlsx-4.0.17 Read, Write and Edit XLSX Files
- optparse-1.4.4 Command Line Option Parser
- org.Hs.eg.db 3.4.2
- pROC-1.10.0 Display and Analyze ROC Curves
- parallelMap-1.3 Unified Interface to Parallelization Back-Ends
- partools-1.1.6 Tools for the ‘Parallel’ Package
- party-1.2-3 A Laboratory for Recursive Partytioning
- pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
- pbkrtest-0.4-7 Parametric Bootstrap and Kenward Roger Based Methods for Mixed
Model Comparison
- pcaMethods 1.70.0
- pcaPP-1.9-72 Robust PCA by Projection Pursuit
- pdist-1.2 Partitioned Distance Function
- pedigree-1.4 Pedigree functions
- pedigreemm-0.3-3 Pedigree-based mixed-effects models
- penalized-0.9-50 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
- perm-1.0-0.0 Exact or Asymptotic permutation tests
- permute-0.9-4 Functions for Generating Restricted Permutations of Data
- phangorn-2.3.1 Phylogenetic Reconstruction and Analysis
- pheatmap-1.0.8 Pretty Heatmaps
- phylobase-0.8.4 Base Package for Phylogenetic Structures and Comparative Data
- phyloseq 1.22.3
- pim-2.0.1 Fit Probabilistic Index Models
- pixmap-0.4-11 Bitmap Images (``Pixel Maps’’)
- pkgconfig-2.0.1 Private Configuration for ‘R’ Packages
- pkgmaker-0.22 Development Utilities for R Packages
- plogr-0.1-1 The ‘plog’ C++ Logging Library
- plotly-4.7.1 Create Interactive Web Graphics via ‘plotly.js’
- plotrix-3.6-6 Various Plotting Functions
- pls-2.6-0 Partial Least Squares and Principal Component Regression
- plyr-1.8.4 Tools for Splitting, Applying and Combining Data
- png-0.1-7 Read and write PNG images
- polspline-1.1.12 Polynomial Spline Routines
- polyclip-1.6-1 Polygon Clipping
- polyester 1.14.0
- polynom-1.3-9 A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulations
- prabclus-2.2-6 Functions for Clustering of Presence-Absence, Abundance and
Multilocus Genetic Data
- pracma-2.0.7 Practical Numerical Math Functions
- praise-1.0.0 Praise Users
- preprocessCore 1.40.0
- prettyunits-1.0.2 Pretty, Human Readable Formatting of Quantities
- prodlim-1.6.1 Product-Limit Estimation for Censored Event History Analysis
- profileModel-0.5-9 Tools for profiling inference functions for various model<U+000a>classes
- progress-1.1.2 Terminal Progress Bars
- proto-1.0.0 Prototype Object-Based Programming
- pscl-1.5.2 Political Science Computational Laboratory
- pspline-1.0-18 Penalized Smoothing Splines
- psych-1.7.8 Procedures for Psychological, Psychometric, and Personality
Research
- psychotools-0.4-2 Psychometric Modeling Infrastructure
- purrr-0.2.4 Functional Programming Tools
- pvclust-2.0-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
- qgraph-1.4.4 Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
- qtl-1.41-6 Tools for Analyzing QTL Experiments
- quadprog-1.5-5 Functions to solve Quadratic Programming Problems.
- quantmod-0.4-11 Quantitative Financial Modelling Framework
- quantreg-5.34 Quantile Regression
- quantsmooth 1.44.0
- qvalue-2.10.0 Q-value estimation for false discovery rate control
- qvcalc-0.9-1 Quasi Variances for Factor Effects in Statistical Models
- rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
- rAzureBatch 0.5.1
- rGADEM 2.26.0
- rJava-0.9-9 Low-Level R to Java Interface
- randomForest-4.6-12 Breiman and Cutler’s Random Forests for Classification and
Regression
- randomForestSRC-2.5.1 Random Forests for Survival, Regression, and Classification
(RF-SRC)
- rappdirs-0.3.1 Application Directories: Determine Where to Save Data, Caches,
and Logs
- raster-2.5-8 Geographic Data Analysis and Modeling
- readr-1.1.1 Read Rectangular Text Data
- readxl-1.0.0 Read Excel Files
- recipes-0.1.0 Preprocessing Tools to Create Design Matrices
- registry-0.3 Infrastructure for R Package Registries
- regress-1.3-15 Gaussian Linear Models with Linear Covariance Structure
- regtools-1.0.1 Regression Tools
- relations-0.6-7 Data Structures and Algorithms for Relations
- relevent-1.0-4 Relational Event Models
- rematch-1.0.1 Match Regular Expressions with a Nicer ‘API’
- rentrez-1.1.0 ‘Entrez’ in R
- repr-0.12.0 Serializable Representations
- reshape-0.8.7 Flexibly Reshape Data
- reshape2-1.4.2 Flexibly Reshape Data: A Reboot of the Reshape Package
- rex-1.1.2 Friendly Regular Expressions
- rgenoud-5.8-1.0 R Version of GENetic Optimization Using Derivatives
- rgexf-0.15.3 Build, Import and Export GEXF Graph Files
- rgl-0.98.1 3D Visualization Using OpenGL
- rhdf5 2.22.0
- ritis-0.7.0 Integrated Taxonomic Information System Client
- rjags-4-6 Bayesian Graphical Models using MCMC
- rjson-0.2.15 JSON for R
- rlang-0.1.4 Functions for Base Types and Core R and ‘Tidyverse’ Features
- rlecuyer-0.3-4 R Interface to RNG with Multiple Streams
- rmarkdown-1.6 Dynamic Documents for R
- rmeta-2.16 Meta-Analysis
- rms-5.1-1 Regression Modeling Strategies
- rncl-0.8.2 An Interface to the Nexus Class Library
- rngtools-1.2.4 Utility Functions for Working with Random Number Generators
- robustbase-0.92-8 Basic Robust Statistics
- rootSolve-1.7 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
- rotl-3.0.3 Interface to the ‘Open Tree of Life’ API
- roxygen2-6.0.1 In-Line Documentation for R
- rpart-4.1-11 Recursive Partitioning and Regression Trees
- rprojroot-1.2 Finding Files in Project Subdirectories
- rrcov-1.4-3 Scalable Robust Estimators with High Breakdown Point
- rredlist-0.4.0 ‘IUCN’ Red List Client
- rslurm-0.4.0 Submit R Calculations to a Slurm Cluster
- rstan-2.16.2 R Interface to Stan
- rstudioapi-0.7 Safely Access the RStudio API
- rtracklayer 1.38.0
- rversions-1.0.3 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
- rzmq-0.9.3 R Bindings for ‘ZeroMQ’
- samr-2.0 SAM: Significance Analysis of Microarrays
- sandwich-2.4-0 Robust Covariance Matrix Estimators
- scales-0.5.0 Scale Functions for Visualization
- scatterplot3d-0.3-40 3D Scatter Plot
- scidb-2.0.0 An R Interface to SciDB
- segmented-0.5-2.2 Regression Models with Break-Points / Change-Points Estimation
- sem-3.1-9 Structural Equation Models
- sendmailR-1.2-1 send email using R
- seqLogo 1.44.0
- seqinr-3.4-5 Biological Sequences Retrieval and Analysis
- sets-1.0-17 Sets, Generalized Sets, Customizable Sets and Intervals
- sfsmisc-1.1-1 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
- shape-1.4.3 Functions for Plotting Graphical Shapes, Colors
- shapefiles-0.7 Read and Write ESRI Shapefiles
- shiny-1.0.5 Web Application Framework for R
- shinycssloaders-0.2.0 Add CSS Loading Animations to ‘shiny’ Outputs
- shinydashboard-0.6.1 Create Dashboards with ‘Shiny’
- sigaR 1.26.0
- siggenes 1.52.0
- slam-0.1-40 Sparse Lightweight Arrays and Matrices
- sm-2.2-5.4 Smoothing Methods for Nonparametric Regression and Density
Estimation
- sna-2.4 Tools for Social Network Analysis
- snow-0.4-2 Simple Network of Workstations
- snowfall-1.84-6.1 Easier cluster computing (based on snow).
- snpStats 1.28.0
- solrium-1.0.0 General Purpose R Interface to ‘Solr’
- som-0.3-5.1 Self-Organizing Map
- sourcetools-0.1.6 Tools for Reading, Tokenizing and Parsing R Code
- sp-1.2-5 Classes and Methods for Spatial Data
- spam-2.1-1 SPArse Matrix
- sparklyr-0.6.4 R Interface to Apache Spark
- spatial-7.3-11 Functions for Kriging and Point Pattern Analysis
- spatstat-1.53-2 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
- spatstat.data-1.1-1 Datasets for ‘spatstat’
- spatstat.utils-1.7-1 Utility Functions for ‘spatstat’
- spdep-0.6-15 Spatial Dependence: Weighting Schemes, Statistics and Models
- splines built in
- sqldf-0.4-11 Manipulate R Data Frames Using SQL
- stabledist-0.7-1 Stable Distribution Functions
- stabs-0.6-3 Stability Selection with Error Control
- statmod-1.4.30 Statistical Modeling
- statnet-2016.9 Software Tools for the Statistical Analysis of Network Data
- statnet.common-4.0.0 Common R Scripts and Utilities Used by the Statnet Project
Software
- stats built in
- stats4 built in
- stringdist-0.9.4.6 Approximate String Matching and String Distance Functions
- stringi-1.1.5 Character String Processing Facilities
- stringr-1.2.0 Simple, Consistent Wrappers for Common String Operations
- strucchange-1.5-1 Testing, Monitoring, and Dating Structural Changes
- subplex-1.4-1 Unconstrained Optimization using the Subplex Algorithm
- survey-3.32-1 Analysis of Complex Survey Samples
- survival-2.41-3 Survival Analysis
- survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
- synapseClient 1.13-4
- tables-0.8 Formula-Driven Table Generation
- taxize-0.9.0 Taxonomic Information from Around the Web
- tensor-1.5 Tensor product of arrays
- tensorA-0.36 Advanced tensors arithmetic with named indices
- tergm-3.4.1 Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
- testthat-1.0.2 Unit Testing for R
- tibble-1.3.4 Simple Data Frames
- tidyr-0.7.2 Easily Tidy Data with ‘spread()’ and ‘gather()’ Functions
- tidyselect-0.2.3 Select from a Set of Strings
- tiff-0.1-5 Read and write TIFF images
- tilingArray 1.56.0
- timeDate-3012.100 Rmetrics - Chronological and Calendar Objects
- timeSeries-3022.101.2 Rmetrics - Financial Time Series Objects
- timereg-1.9.1 Flexible Regression Models for Survival Data
- tkWidgets 1.56.0
- tkrplot-0.0-23 TK Rplot
- tm-0.7-1 Text Mining Package
- tmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distribution
- tools built in
- tree-1.0-37 Classification and Regression Trees
- triebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’
- trimcluster-0.1-2 Cluster analysis with trimming
- tripack-1.3-8 Triangulation of Irregularly Spaced Data
- trust-0.1-7 Trust Region Optimization
- tseries-0.10-42 Time Series Analysis and Computational Finance
- tseriesChaos-0.1-13 Analysis of nonlinear time series
- unbalanced-2.0 Racing for Unbalanced Methods Selection
- urca-1.3-0 Unit Root and Cointegration Tests for Time Series Data
- urltools-1.6.0 Vectorised Tools for URL Handling and Parsing
- utils built in
- uuid-0.1-2 Tools for generating and handling of UUIDs
- vcd-1.4-3 Visualizing Categorical Data
- vegan-2.4-4 Community Ecology Package
- venn-1.2 Draw Venn Diagrams
- vioplot-0.2 Violin plot
- viridis-0.4.0 Default Color Maps from ‘matplotlib’
- viridisLite-0.2.0 Default Color Maps from ‘matplotlib’ (Lite Version)
- visNetwork-2.0.1 Network Visualization using ‘vis.js’ Library
- vsn 3.46.0
- waveslim-1.7.5 Basic wavelet routines for one-, two- and three-dimensional<U+000a>signal processing
- wavethresh-4.6.8 Wavelets Statistics and Transforms
- whisker-0.3-2 for R, logicless templating
- widgetTools 1.56.0
- wikitaxa-0.1.4 Taxonomic Information from ‘Wikipedia’
- withr-2.1.0 Run Code ‘With’ Temporarily Modified Global State
- worrms-0.2.0 World Register of Marine Species (WoRMS) Client
- xlsx-0.5.7 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
- xlsxjars-0.6.1 Package required POI jars for the xlsx package
- xml2-1.1.1 Parse XML
- xtable-1.8-2 Export Tables to LaTeX or HTML
- xts-0.10-0 eXtensible Time Series
- yaml-2.1.14 Methods to Convert R Data to YAML and Back
- zlibbioc 1.24.0
- zoo-1.8-0 S3 Infrastructure for Regular and Irregular Time Series (Z’s
Ordered Observations)