R-3.5.3-foss-2016b-fh1

Known Issues

• None

  Package List

• ADGofTest-0.3 Anderson-Darling GoF test
• ALDEx2-1.14.1 Analysis Of Differential Abundance Taking Sample Variation Into Account
• ASCAT 2.5.2
• AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.
• AgiMicroRna-2.32.0 Processing and Differential Expression Analysis of Agilent microRNA chips
• AlgDesign-1.1-7.3 Algorithmic Experimental Design
• AnnotationDbi-1.44.0 Annotation Database Interface
• AnnotationFilter-1.6.0 Facilities for Filtering Bioconductor Annotation Resources
• AnnotationForge-1.24.0 Code for Building Annotation Database Packages
• AnnotationHub-2.14.4 Client to access AnnotationHub resources
• BB-2014.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
• BBmisc-1.11 Miscellaneous Helper Functions for B. Bischl
• BDgraph-2.55 Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
• BH-1.69.0-1 Boost C++ Header Files
• BSgenome-1.50.0 Software infrastructure for efficient representation of full genomes and their SNPs
• BSgenome.Hsapiens.UCSC.hg19-1.4.0 Full genome sequences for Homo sapiens (UCSC version hg19)
• BatchJobs-1.7 Batch Computing with R
• BayesianTools-0.1.6 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-2.42.0 Biobase: Base functions for Bioconductor
• BiocGenerics-0.28.0 S4 generic functions for Bioconductor
• BiocInstaller-1.32.1 Install/Update Bioconductor, CRAN, and github Packages
• BiocManager-1.30.4 Access the Bioconductor Project Package Repository
• BiocParallel-1.16.6 Bioconductor facilities for parallel evaluation
• Biostrings-2.50.2 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
• BradleyTerry2-1.0-9 Bradley-Terry Models
• Brobdingnag-1.2-6 Very Large Numbers in R
• CGEN-3.18.0 An R package for analysis of case-control studies in genetic epidemiology
• CGHbase-1.42.0 CGHbase: Base functions and classes for arrayCGH data analysis.
• CVST-0.2-2 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-2.48.1 Category Analysis
• ComICS-1.0.4 Computational Methods for Immune Cell-Type Subsets
• CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
• DAAG-1.22.1 Data Analysis and Graphics Data and Functions
• DBI-1.0.0 R Database Interface
• DEGseq-1.36.1 Identify Differentially Expressed Genes from RNA-seq data
• DESeq-1.34.1 Differential gene expression analysis based on the negative binomial distribution
• DESeq2-1.22.2 Differential gene expression analysis based on the negative binomial distribution
• DEoptimR-1.0-8 Differential Evolution Optimization in Pure R
• DHARMa-0.2.4 Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
• DNAcopy-1.56.0 DNA copy number data analysis
• DRR-0.0.3 Dimensionality Reduction via Regression
• DT-0.5 A Wrapper of the JavaScript Library ‘DataTables’
• DTRreg-1.3 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, and Q-Learning
• DelayedArray-0.8.0 Delayed operations on array-like objects
• DelayedMatrixStats-1.4.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
• Deriv-3.8.5 Symbolic Differentiation
• DiagrammeR-1.0.0 Graph/Network Visualization
• DiffBind-2.10.0 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-1.60.0 Dynamic document tools
• EBImage-4.24.0 Image processing and analysis toolbox for R
• EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
• EpiModel-1.7.2 Mathematical Modeling of Infectious Disease Dynamics
• FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
• FME-1.3.5 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-1.41 Multivariate Exploratory Data Analysis and Data Mining
• Formula-1.2-3 Extended Model Formulas
• GENESIS-2.12.4 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
• GEOquery-2.50.5 Get data from NCBI Gene Expression Omnibus (GEO)
• GGally-1.4.0 Extension to ‘ggplot2’
• GO.db-3.7.0 A set of annotation maps describing the entire Gene Ontology
• GOstats-2.48.0 Tools for manipulating GO and microarrays
• GSA-1.03.1 Gene Set Analysis
• GSEABase-1.44.0 Gene set enrichment data structures and methods
• GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
• GWASTools-1.28.0 Tools for Genome Wide Association Studies
• GeneNet-1.2.13 Modeling and Inferring Gene Networks
• GenomeGraphs-1.42.0 Plotting genomic information from Ensembl
• GenomeInfoDb-1.18.2 Utilities for manipulating chromosome and other ‘seqname’ identifiers
• GenomeInfoDbData-1.2.0 Species and taxonomy ID look up tables used by GenomeInfoDb
• GenomicAlignments-1.18.1 Representation and manipulation of short genomic alignments
• GenomicFeatures-1.34.4 Tools for making and manipulating transcript centric annotations
• GenomicFiles-1.18.0 Distributed computing by file or by range
• GenomicRanges-1.34.0 Representation and manipulation of genomic intervals and variables defined along a genome
• GetoptLong-0.1.7 Parsing Command-Line Arguments and Variable Interpolation
• GillespieSSA-0.5-4 Gillespie’s Stochastic Simulation Algorithm (SSA)
• GlobalOptions-0.1.0 Generate Functions to Get or Set Global Options
• Gviz-1.26.5 Plotting data and annotation information along genomic coordinates
• HCsnip 1.16.0
• HDF5Array-1.10.1 HDF5 backend for DelayedArray objects
• HMMcopy-1.24.0 Copy number prediction with correction for GC and mappability bias for HTS data
• HWxtest-1.1.7 Exact Tests for Hardy-Weinberg Proportions
• HaploSim-1.8.4 Functions to simulate haplotypes
• Hmisc-4.2-0 Harrell Miscellaneous
• Homo.sapiens-1.3.1 Annotation package for the Homo.sapiens object
• IDPmisc-1.1.19 ‘Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)’
• IRanges-2.16.0 Infrastructure for manipulating intervals on sequences
• IRdisplay-0.7.0 ‘Jupyter’ Display Machinery
• IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
• Iso-0.0-17 Functions to Perform Isotonic Regression
• JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J. Buttlar
• KEGG.db-3.2.3 A set of annotation maps for KEGG
• KEGGREST-1.22.0 Client-side REST access to KEGG
• KEGGgraph-1.42.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
• KEGGprofile-1.24.0 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-2.23-15 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
• LearnBayes-2.15.1 Functions for Learning Bayesian Inference
• Lmoments-1.2-3 L-Moments and Quantile Mixtures
• LogicReg-1.5.10 Logic Regression
• LymphoSeq-1.10.0 Analyze high-throughput sequencing of T and B cell receptors
• LymphoSeqDB-0.99.2 LymphoSeq annotation databases
• MASS-7.3-51.1 Support Functions and Datasets for Venables and Ripley’s MASS
• MCMCglmm-2.28 MCMC Generalised Linear Mixed Models
• MCMCpack-1.4-4 Markov Chain Monte Carlo (MCMC) Package
• MPV-1.53 Data Sets from Montgomery, Peck and Vining
• MatchIt-3.0.2 Nonparametric Preprocessing for Parametric Causal Inference
• Matching-4.9-5 Multivariate and Propensity Score Matching with Balance Optimization
• Matrix-1.2-16 Sparse and Dense Matrix Classes and Methods
• MatrixModels-0.4-1 Modelling with Sparse And Dense Matrices
• Mfuzz-2.42.0 Soft clustering of time series gene expression data
• ModelMetrics-1.2.2 Rapid Calculation of Model Metrics
• MotIV-1.38.0 Motif Identification and Validation
• NLP-0.2-0 Natural Language Processing Infrastructure
• NMF-0.21.0 Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
• NOISeq-2.26.1 Exploratory analysis and differential expression for RNA-seq data
• OceanView-1.0.4 Visualisation of Oceanographic Data and Model Output
• OrganismDbi-1.24.0 Software to enable the smooth interfacing of different database packages
• PBSddesolve-1.12.4 Solver for Delay Differential Equations
• PFAM.db-3.7.0 A set of protein ID mappings for PFAM
• PICS-2.26.0 Probabilistic inference of ChIP-seq
• PKI-0.1-5.1 Public Key Infrastucture for R Based on the X.509 Standard
• ParamHelpers-1.12 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-1.0-2 Polynomials in R
• ProtGenerics-1.14.0 S4 generic functions for Bioconductor proteomics infrastructure
• R.cache-0.13.0 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.methodsS3-1.7.1 S3 Methods Simplified
• R.oo-1.22.0 R Object-Oriented Programming with or without References
• R.rsp-0.43.1 Dynamic Generation of Scientific Reports
• R.utils-2.8.0 Various Programming Utilities
• R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
• R2jags-0.5-7 Using R to Run ‘JAGS’
• R6-2.4.0 Encapsulated Classes with Reference Semantics
• RANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
• RBGL-1.58.1 An interface to the BOOST graph library
• RCircos-1.2.0 Circos 2D Track Plot
• RColorBrewer-1.1-2 ColorBrewer Palettes
• RCurl-1.95-4.12 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
• RInside-0.2.15 C++ Classes to Embed R in C++ Applications
• RItools-0.1-16 Randomization Inference Tools
• RJSONIO-1.3-1.1 Serialize R Objects to JSON, JavaScript Object Notation
• RLRsim-3.1-3 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models
• RMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>Theory
• RMySQL-0.10.17 Database Interface and ‘MySQL’ Driver for R
• RNASeqPower-1.22.1 Sample size for RNAseq studies
• RNeXML-2.3.0 Semantically Rich I/O for the ‘NeXML’ Format
• ROCR-1.0-7 Visualizing the Performance of Scoring Classifiers
• RPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database System
• RProtoBufLib-1.4.0 C++ headers and static libraries of Protocol buffers
• RSNNS-0.4-11 Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
• RSQLite-2.1.1 ‘SQLite’ Interface for R
• RSclient-0.7-3 Client for Rserve
• RSpectra-0.13-1 Solvers for Large-Scale Eigenvalue and SVD Problems
• RUnit-0.4.32 R Unit Test Framework
• RWeka-0.4-40 R/Weka Interface
• RWekajars-3.9.3-1 R/Weka Interface Jars
• Rcpp-1.0.0 Seamless R and C++ Integration
• RcppArmadillo-0.9.200.7.1 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library
• RcppEigen-0.3.3.5.0 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra Library
• RcppGSL-0.3.6 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and Matrices
• RcppParallel-4.4.2 Parallel Programming Tools for ‘Rcpp’
• RcppProgress-0.4.1 An Interruptible Progress Bar with OpenMP Support for C++ in R Packages
• RcppRoll-0.3.0 Efficient Rolling / Windowed Operations
• Rdpack-0.10-1 Update and Manipulate Rd Documentation Objects
• ReportingTools-2.22.1 Tools for making reports in various formats
• Rglpk-0.6-4 R/GNU Linear Programming Kit Interface
• Rgraphviz-2.26.0 Provides plotting capabilities for R graph objects
• Rhdf5lib-1.4.2 hdf5 library as an R package
• Rhpc-0.18-204 Permits *apply() Style Dispatch for ‘HPC’
• Ringo-1.46.0 R Investigation of ChIP-chip Oligoarrays
• Rlabkey-2.2.4 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-1.34.1 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
• Rssa-1.0 A Collection of Methods for Singular Spectrum Analysis
• Rsubread-1.32.4 Subread sequence alignment and counting for R
• Rtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
• Rttf2pt1-1.3.7 ‘ttf2pt1’ Program
• S4Vectors-0.20.1 S4 implementation of vector-like and list-like objects
• SDMTools-1.1-221 Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
• SKAT-1.3.2.1 SNP-Set (Sequence) Kernel Association Test
• SNPRelate-1.16.0 Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)
• SPIA-2.34.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
• SQUAREM-2017.10-1 Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
• SeqArray-1.22.6 Data Management of Large-scale Whole-genome Sequence Variant Calls
• SeqVarTools-1.20.2 Tools for variant data
• ShortRead-1.40.0 FASTQ input and manipulation
• SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
• SparseM-1.77 Sparse Linear Algebra
• StanHeaders-2.18.1 C++ Header Files for Stan
• SummarizedExperiment-1.12.0 SummarizedExperiment container
• SuperLearner-2.0-24 Super Learner Prediction
• SuppDists-1.1-9.4 Supplementary Distributions
• TH.data-1.0-10 TH’s Data Archive
• TMB-1.7.15 Template Model Builder: A General Random Effect Tool Inspired by ‘ADMB’
• TTR-0.23-4 Technical Trading Rules
• TeachingDemos-2.10 Demonstrations for Teaching and Learning
• TitanCNA-1.20.1 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
• TraMineR-2.0-10 Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
• TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)
• UpSetR-1.3.3 A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
• VGAM-1.1-1 Vector Generalized Linear and Additive Models
• VIM-4.8.0 Visualization and Imputation of Missing Values
• VariantAnnotation-1.28.11 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
• WriteXLS-4.1.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files
• XML-3.98-1.19 Tools for Parsing and Generating XML Within R and S-Plus
• XVector-0.22.0 Representation and manipulation of external sequences
• 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-4.2 Applies Multiclass AdaBoost.M1, SAMME and Bagging
• ade4-1.7-13 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
• adegenet-2.1.1 Exploratory Analysis of Genetic and Genomic Data
• adephylo-1.1-11 Exploratory Analyses for the Phylogenetic Comparative Method
• affy-1.60.0 Methods for Affymetrix Oligonucleotide Arrays
• affycoretools-1.54.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
• affyio-1.52.0 Tools for parsing Affymetrix data files
• aggregation-1.0.1 p-Value Aggregation Methods
• akima-0.6-2 Interpolation of Irregularly and Regularly Spaced Data
• alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
• amap-0.8-16 Another Multidimensional Analysis Package
• animation-2.6 A Gallery of Animations in Statistics and Utilities to Create Animations
• annaffy-1.54.0 Annotation tools for Affymetrix biological metadata
• annotate-1.60.1 Annotation for microarrays
• aod-1.3.1 Analysis of Overdispersed Data
• ape-5.2 Analyses of Phylogenetics and Evolution
• argparser-0.4 Command-Line Argument Parser
• arm-1.10-1 Data Analysis Using Regression and Multilevel/Hierarchical Models
• askpass-1.1 Safe Password Entry for R, Git, and SSH
• assertthat-0.2.0 Easy Pre and Post Assertions
• audio-0.1-5.1 Audio Interface for R
• aws.ec2metadata-0.1.5 Get EC2 Instance Metadata
• aws.s3-0.3.12 ‘AWS S3’ Client Package
• aws.signature-0.4.4 Amazon Web Services Request Signatures
• backports-1.1.3 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-2.16.0 Empirical Bayesian analysis of patterns of differential expression in count data
• bayesm-3.1-1 Bayesian Inference for Marketing/Micro-Econometrics
• bdsmatrix-1.3-3 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 Bibtex Parser
• biglm-0.9-1 bounded memory linear and generalized linear models
• bigmemory-4.5.33 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-2.3-4 Biological Structure Analysis
• biom-0.3.12 An interface package (beta) for the BIOM file format.
• biomaRt-2.38.0 Interface to BioMart databases (i.e. Ensembl)
• biovizBase-1.30.1 Basic graphic utilities for visualization of genomic data.
• bit-1.1-14 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-1.1.1 A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’)
• bmp-0.3 Read Windows Bitmap (BMP) Images
• bnlearn-4.4.1 Bayesian Network Structure Learning, Parameter Learning and Inference
• bold-0.8.6 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”
• breakaway-3.0 Species Richness Estimation and Modeling
• brew-1.0-6 Templating Framework for Report Generation
• brglm-0.6.1 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-0.6-0 Bridge Sampling for Marginal Likelihoods and Bayes Factors
• broom-0.5.1 Convert Statistical Analysis Objects into Tidy Tibbles
• bst-0.3-17 Gradient Boosting
• bumphunter-1.24.5 Bump Hunter
• caTools-1.17.1.2 Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
• calibrate-1.7.2 Calibration of Scatterplot and Biplot Axes
• callr-3.1.1 Call R from R
• car-3.0-2 Companion to Applied Regression
• carData-3.0-2 Companion to Applied Regression Data Sets
• caret-6.0-81 Classification and Regression Training
• catdata-1.2.1 Categorical Data
• cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
• cgdsr-1.2.10 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-1.9.1 Fast and Versatile Argument Checks
• chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
• chipseq-1.32.0 chipseq: A package for analyzing chipseq data
• chron-2.3-53 Chronological Objects which can Handle Dates and Times
• circlize-0.4.5 Circular Visualization
• clValid-0.6-6 Validation of Clustering Results
• class-7.3-15 Functions for Classification
• classInt-0.3-1 Choose Univariate Class Intervals
• cli-1.0.1 Helpers for Developing Command Line Interfaces
• clipr-0.5.0 Read and Write from the System Clipboard
• clisymbols-1.2.0 Unicode Symbols at the R Prompt
• clue-0.3-57 Cluster Ensembles
• cluster-2.0.7-1 “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-0.3.0 Visualise Clusterings at Different Resolutions
• coda-0.19-2 Output Analysis and Diagnostics for MCMC
• codetools-0.2-16 Code Analysis Tools for R
• coin-1.3-0 Conditional Inference Procedures in a Permutation Test Framework
• colorspace-1.4-0 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-1.40-2 Compositional Data Analysis
• config-0.3 Manage Environment Specific Configuration Values
• copula-0.999-19 Multivariate Dependence with Copulas
• corpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlation
• cowplot-0.9.4 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
• coxme-2.2-10 Mixed Effects Cox Models
• crayon-1.3.4 Colored Terminal Output
• crosstalk-1.0.0 Inter-Widget Interactivity for HTML Widgets
• crul-0.7.0 HTTP Client
• csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
• cubature-2.0.3 Adaptive Multivariate Integration over Hypercubes
• cummeRbund-2.24.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
• curl-3.3 A Modern and Flexible Web Client for R
• cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
• cytolib-1.4.1 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
• dada2-1.10.1 Accurate, high-resolution sample inference from amplicon sequencing data
• data.table-1.12.0 Extension of data.frame
• datasets built in
• dbplyr-1.3.0 A ‘dplyr’ Back End for Databases
• ddalpha-1.3.8 Depth-Based Classification and Calculation of Data Depth
• deSolve-1.21 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-0.1-16 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
• dendextend-1.9.0 Extending ‘dendrogram’ Functionality in R
• derfinder-1.16.1 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
• derfinderHelper-1.16.1 derfinder helper package
• desc-1.2.0 Manipulate DESCRIPTION Files
• descr-1.1.4 Descriptive Statistics
• devtools-2.0.1 Tools to Make Developing R Packages Easier
• dfoptim-2018.2-1 Derivative-Free Optimization
• diagram-1.6.4 Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
• diamonds-1.0-5 Analysis and sampling grids from diamond partitions
• dichromat-2.0-0 Color Schemes for Dichromats
• digest-0.6.18 Create Compact Hash Digests of R Objects
• dimRed-0.2.2 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
• distr-2.7.0 Object Oriented Implementation of Distributions
• distrEx-2.7.0 Extensions of Package ‘distr’
• diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis Package
• doMC-1.3.5 Foreach Parallel Adaptor for ‘parallel’
• doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
• doParallel-1.0.14 Foreach Parallel Adaptor for the ‘parallel’ Package
• doRNG-1.7.1 Generic Reproducible Parallel Backend for ‘foreach’ Loops
• doSNOW-1.0.16 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-0.8.0.1 A Grammar of Data Manipulation
• dtangle-0.3.1 Cell Type Deconvolution from Gene Expressions
• dtw-1.20-1 Dynamic Time Warping Algorithms
• dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
• dynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering Dendrograms
• e1071-1.7-0.1 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
• edgeR-3.24.3 Empirical Analysis of Digital Gene Expression Data in R
• elasticnet-1.1.1 Elastic-Net for Sparse Estimation and Sparse PCA
• ellipse-0.4.1 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
• ellipsis-0.1.0 Tools for Working with …
• emulator-1.2-19 Bayesian Emulation of Computer Programs
• energy-1.7-5 E-Statistics: Multivariate Inference via the Energy of Data
• ensembldb-2.6.7 Utilities to create and use Ensembl-based annotation databases
• ergm-3.9.4 Fit, Simulate and Diagnose Exponential-Family Models for Networks
• ergm.count-3.3.0 Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
• evaluate-0.13 Parsing and Evaluation Tools that Provide More Details than the Default
• expm-0.999-3 Matrix Exponential, Log, ‘etc’
• expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
• extRemes-2.0-9 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-0.4.0 ANSI Control Sequence Aware String Functions
• farver-1.1.0 Vectorised Colour Conversion and Comparison
• fastICA-1.2-1 FastICA Algorithms to Perform ICA and Projection Pursuit
• fastcluster-1.1.25 Fast Hierarchical Clustering Routines for R and ‘Python’
• fastmatch-1.1-0 Fast match() function
• fastseg-1.28.0 fastseg - a fast segmentation algorithm
• fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
• fda-2.4.8 Functional Data Analysis
• fdrtool-1.2.15 Estimation of (Local) False Discovery Rates and Higher Criticism
• feather-0.3.2 R Bindings to the Feather ‘API’
• ff-2.2-14 Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
• ffbase-0.12.7 Basic Statistical Functions for Package ‘ff’
• fftw-1.0-5 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-9.6 Tools for Spatial Data
• filehash-2.4-1 Simple Key-Value Database
• fishMod-0.29 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta Log-Normal Models
• fit.models-0.5-14 Compare Fitted Models
• fitdistrplus-1.0-14 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-3.20.1 Clustering for Flow Cytometry
• flowCore-1.48.1 flowCore: Basic structures for flow cytometry data
• flowStats-3.40.1 Statistical methods for the analysis of flow cytometry data
• flowViz-1.46.1 Visualization for flow cytometry
• flowWorkspace-3.30.2 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
• fma-2.3 Data Sets from “Forecasting: Methods and Applications” by Makridakis, Wheelwright & Hyndman (1998)
• forcats-0.4.0 Tools for Working with Categorical Variables (Factors)
• foreach-1.4.4 Provides Foreach Looping Construct for R
• forecast-8.5 Forecasting Functions for Time Series and Linear Models
• foreign-0.8-71 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …
• forge-0.2.0 Casting Values into Shape
• formatR-1.6 Format R Code Automatically
• fossil-0.3.7 Palaeoecological and Palaeogeographical Analysis Tools
• fpc-2.1-11.1 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
• fs-1.2.6 Cross-Platform File System Operations Based on ‘libuv’
• fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
• futile.logger-1.4.3 A Logging Utility for R
• futile.options-1.0.1 Futile Options Management
• future-1.12.0 Unified Parallel and Distributed Processing in R for Everyone
• gage-2.32.1 Generally Applicable Gene-set Enrichment for Pathway Analysis
• gam-1.16 Generalized Additive Models
• gamlss-5.1-2 Generalised Additive Models for Location Scale and Shape
• gamlss.data-5.1-0 GAMLSS Data
• gamlss.dist-5.1-1 Distributions for Generalized Additive Models for Location Scale and Shape
• gamlss.tr-5.1-0 Generating and Fitting Truncated `gamlss.family’ Distributions
• gamm4-0.2-5 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
• gap-1.1-22 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-2.54.0 Background Adjustment Using Sequence Information
• gdalUtils-2.0.1.14 Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities
• gdata-2.18.0 Various R Programming Tools for Data Manipulation
• gdistance-1.2-2 Distances and Routes on Geographical Grids
• gdsfmt-1.18.1 R Interface to CoreArray Genomic Data Structure (GDS) files
• gee-4.13-19 Generalized Estimation Equation Solver
• geepack-1.2-1 Generalized Estimating Equation Package
• geiger-2.0.6.1 Analysis of Evolutionary Diversification
• geneLenDataBase-1.18.0 Lengths of mRNA transcripts for a number of genomes
• genefilter-1.64.0 genefilter: methods for filtering genes from high-throughput experiments
• geneplotter-1.60.0 Graphics related functions for Bioconductor
• generics-0.0.2 Common S3 Generics not Provided by Base R Methods Related to Model Fitting
• genoset-1.38.0 A RangedSummarizedExperiment with methods for copy number analysis
• geometry-0.4.0 Mesh Generation and Surface Tessellation
• getopt-1.20.2 C-Like ‘getopt’ Behavior
• ggExtra-0.8 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’ Enhancements
• ggbeeswarm-0.6.0 Categorical Scatter (Violin Point) Plots
• ggbio-1.30.0 Visualization tools for genomic data
• ggforce-0.2.0 Accelerating ‘ggplot2’
• ggm-2.3 Functions for graphical Markov models
• ggplot2-3.1.0 Create Elegant Data Visualisations Using the Grammar of Graphics
• ggraph-1.0.2 An Implementation of Grammar of Graphics for Graphs and Networks
• ggrepel-0.8.0 Automatically Position Non-Overlapping Text Labels with ‘ggplot2’
• ggridges-0.5.1 Ridgeline Plots in ‘ggplot2’
• ggthemes-4.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’
• ggtree-1.14.6 an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
• ggvis-0.4.4 Interactive Grammar of Graphics
• gh-1.0.1 ‘GitHub’ ‘API’
• git2r-0.24.0 Provides Access to Git Repositories
• glasso-1.10 Graphical Lasso: Estimation of Gaussian Graphical Models
• gllvm-1.1.2 Generalized Linear Latent Variable Models
• glmmML-1.0.3 Generalized Linear Models with Clustering
• glmmTMB-0.2.3 Generalized Linear Mixed Models using Template Model Builder
• glmnet-2.0-16 Lasso and Elastic-Net Regularized Generalized Linear Models
• glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model
• globals-0.12.4 Identify Global Objects in R Expressions
• glue-1.3.0 Interpreted String Literals
• gmm-1.6-2 Generalized Method of Moments and Generalized Empirical Likelihood
• gmodels-2.18.1 Various R Programming Tools for Model Fitting
• goftest-1.1-1 Classical Goodness-of-Fit Tests for Univariate Distributions
• gomms-1.0 GLM-Based Ordination Method
• goseq-1.34.1 Gene Ontology analyser for RNA-seq and other length biased data
• gower-0.2.0 Gower’s Distance
• gplots-3.0.1.1 Various R Programming Tools for Plotting Data
• grDevices built in
• graph-1.60.0 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
• grpreg-3.2-1 Regularization Paths for Regression Models with Grouped Covariates
• gsalib-2.1 Utility Functions For GATK
• gsl-1.9-10.3 Wrapper for the Gnu Scientific Library
• gsubfn-0.7 Utilities for Strings and Function Arguments
• gsw-1.0-5 Gibbs Sea Water Functions
• gtable-0.2.0 Arrange ‘Grobs’ in Tables
• gtools-3.8.1 Various R Programming Tools
• hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
• haplo.stats-1.7.9 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
• haven-2.1.0 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
• hdf5r-1.0.1 Interface to the ‘HDF5’ Binary Data Format
• heatmap3-1.1.1 An Improved Heatmap Package
• hexbin-1.27.2 Hexagonal Binning Routines
• hgu133plus2.db-3.2.3 Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2)
• highr-0.7 Syntax Highlighting for R Source Code
• hms-0.4.2 Pretty Time of Day
• hopach-2.42.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
• htmlTable-1.13.1 Advanced Tables for Markdown/HTML
• htmltools-0.3.6 Tools for HTML
• htmlwidgets-1.3 HTML Widgets for R
• httpcode-0.2.0 ‘HTTP’ Status Code Helper
• httpuv-1.4.5.1 HTTP and WebSocket Server Library
• httr-1.4.0 Tools for Working with URLs and HTTP
• huge-1.3.0 High-Dimensional Undirected Graph Estimation
• hwriter-1.3.2 HTML Writer - Outputs R objects in HTML format
• ica-1.0-2 Independent Component Analysis
• idr-1.2 Irreproducible discovery rate
• igraph-1.2.4 Network Analysis and Visualization
• igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
• illuminaio-0.24.0 Parsing Illumina Microarray Output Files
• imager-0.41.2 Image Processing Library Based on ‘CImg’
• impute-1.56.0 impute: Imputation for microarray data
• ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
• 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-1.20.0 Base package for enabling powerful shiny web displays of Bioconductor objects
• interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
• inum-1.0-0 Interval and Enum-Type Representation of Vectors
• ipred-0.9-8 Improved Predictors
• irace-3.1 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
• iterators-1.0.10 Provides Iterator Construct for R
• itertools-0.1-3 Iterator Tools
• its-1.1.8 Irregular Time Series
• jomo-2.6-7 Multilevel Joint Modelling Multiple Imputation
• jpeg-0.1-8 Read and write JPEG images
• jsonlite-1.6 A Robust, High Performance JSON Parser and Generator for R
• kernlab-0.9-27 Kernel-Based Machine Learning Lab
• kin.cohort-0.7 Analysis of Kin-Cohort Studies
• kinship2-1.6.4 Pedigree Functions
• klaR-0.6-14 Classification and Visualization
• knitr-1.22 A General-Purpose Package for Dynamic Report Generation in R
• kohonen-3.0.8 Supervised and Unsupervised Self-Organising Maps
• ks-1.11.4 Kernel Smoothing
• kyotil-2018.10-17 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
• labelled-2.1.0 Manipulating Labelled Data
• laeken-0.5.0 Estimation of Indicators on Social Exclusion and Poverty
• lambda.r-1.2.3 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-2.9.0 Latent Position and Cluster Models for Statistical Networks
• later-0.8.0 Utilities for Delaying Function Execution
• lattice-0.20-38 Trellis Graphics for R
• latticeExtra-0.6-28 Extra Graphical Utilities Based on Lattice
• lava-1.6.5 Latent Variable Models
• lavaan-0.6-3 Latent Variable Analysis
• lazy-1.2-16 Lazy Learning for Local Regression
• lazyeval-0.2.1 Lazy (Non-Standard) Evaluation
• leaps-3.0 Regression Subset Selection
• lhs-1.0.1 Latin Hypercube Samples
• libcoin-1.0-4 Linear Test Statistics for Permutation Inference
• limSolve-1.5.5.3 Solving Linear Inverse Models
• limma-3.38.3 Linear Models for Microarray Data
• lintr-1.0.3 A ‘Linter’ for R Code
• listenv-0.7.0 Environments Behaving (Almost) as Lists
• lme4-1.1-21 Linear Mixed-Effects Models using ‘Eigen’ and S4
• lmtest-0.9-36 Testing Linear Regression Models
• locfdr-1.1-8 Computes Local False Discovery Rates
• 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-1.23 Firth’s Bias-Reduced Logistic Regression
• logspline-2.1.12 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-1.1-1 Statistics for Long-Memory Processes (Book Jan Beran), and Related Functionality
• lpSolve-5.6.13 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
• lpridge-1.0-8 Local Polynomial (Ridge) Regression
• lsei-1.2-0 Solving Least Squares or Quadratic Programming Problems under Equality/Inequality Constraints
• lubridate-1.7.4 Make Dealing with Dates a Little Easier
• lumi-2.34.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
• maSigPro-1.54.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
• magic-1.5-9 Create and Investigate Magic Squares
• magick-2.0 Advanced Graphics and Image-Processing in R
• magrittr-1.5 A Forward-Pipe Operator for R
• manipulateWidget-0.10.0 Add Even More Interactivity to Interactive Charts
• mapdata-2.3.0 Extra Map Databases
• mapproj-1.2.6 Map Projections
• maps-3.3.0 Draw Geographical Maps
• maptools-0.9-5 Tools for Handling Spatial Objects
• markdown-0.9 Render Markdown with the C Library ‘Sundown’
• marray-1.60.0 Exploratory analysis for two-color spotted microarray data
• matrixStats-0.54.0 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
• matrixcalc-1.0-3 Collection of functions for matrix calculations
• maxLik-1.3-4 Maximum Likelihood Estimation and Related Tools
• mboost-2.9-1 Model-Based Boosting
• mclust-5.4.2 Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
• mcmc-0.9-6 Markov Chain Monte Carlo
• mediation-4.4.6 Causal Mediation Analysis
• memoise-1.1.0 Memoisation of Functions
• memuse-4.0-0 Memory Estimation Utilities
• metagenomeSeq-1.24.1 Statistical analysis for sparse high-throughput sequencing
• metap-1.1 Meta-Analysis of Significance Values
• methods built in
• methylumi-2.28.0 Handle Illumina methylation data
• mets-1.2.5 Analysis of Multivariate Event Times
• mgcv-1.8-27 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
• mi-1.0 Missing Data Imputation and Model Checking
• mice-3.4.0 Multivariate Imputation by Chained Equations
• mime-0.6 Map Filenames to MIME Types
• minfi-1.28.4 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-0.6-22 Miscellaneous Tools and Utilities
• mitml-0.3-7 Tools for Multiple Imputation in Multilevel Modeling
• mixOmics-6.6.2 Omics Data Integration Project
• mixtools-1.1.0 Tools for Analyzing Finite Mixture Models
• mlbench-2.1-1 Machine Learning Benchmark Problems
• mlogit-0.4-1 Multinomial Logit Models
• mlr-2.13 Machine Learning in R
• mnormt-1.5-5 The Multivariate Normal and t Distributions
• modelr-0.1.4 Modelling Functions that Work with the Pipe
• modeltools-0.2-22 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-0.3-7 Regularized Linear Models
• msa-1.14.0 Multiple Sequence Alignment
• msm-1.6.6 Multi-State Markov and Hidden Markov Models in Continuous Time
• multcomp-1.4-10 Simultaneous Inference in General Parametric Models
• multicool-0.1-10 Permutations of Multisets in Cool-Lex Order
• multtest-2.38.0 Resampling-based multiple hypothesis testing
• munsell-0.5.0 Utilities for Using Munsell Colours
• mvabund-4.0.1 Statistical Methods for Analysing Multivariate Abundance Data
• mvtnorm-1.0-10 Multivariate Normal and t Distributions
• natserv-0.3.0 ‘NatureServe’ Interface
• ncbit-2013.03.29 retrieve and build NBCI taxonomic data
• ncdf4-1.16.1 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
• ncdfFlow-2.28.1 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
• ndtv-0.12.3 Network Dynamic Temporal Visualizations
• network-1.14-377 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-3.3.2 Solve Systems of Nonlinear Equations
• nlme-3.1-137 Linear and Nonlinear Mixed Effects Models
• nloptr-1.2.1 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 aka Gaussian (1-d) Mixture Models (S3 Classes and Methods)
• np-0.60-9 Nonparametric Kernel Smoothing Methods for Mixed Data Types
• npsurv-0.4-0 Nonparametric Survival Analysis
• numDeriv-2016.8-1 Accurate Numerical Derivatives
• nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
• oce-1.0-1 Analysis of Oceanographic Data
• oligoClasses-1.44.0 Classes for high-throughput arrays supported by oligo and crlmm
• openCyto-1.20.2 Hierarchical Gating Pipeline for flow cytometry data
• openssl-1.2.2 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
• openxlsx-4.1.0 Read, Write and Edit XLSX Files
• optmatch-0.9-10 Functions for Optimal Matching
• optparse-1.6.1 Command Line Option Parser
• ordinal-2019.3-9 Regression Models for Ordinal Data
• org.Hs.eg.db-3.7.0 Genome wide annotation for Human
• pROC-1.13.0 Display and Analyze ROC Curves
• 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-1.3 Unified Interface to Parallelization Back-Ends
• partools-1.1.6 Tools for the ‘Parallel’ Package
• party-1.3-3 A Laboratory for Recursive Partytioning
• partykit-1.2-3 A Toolkit for Recursive Partytioning
• pastecs-1.3.21 Package for Analysis of Space-Time Ecological Series
• pbapply-1.4-0 Adding Progress Bar to ‘*apply’ Functions
• pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
• pbkrtest-0.4-7 Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison
• pbs-1.1 Periodic B Splines
• pcaMethods-1.74.0 A collection of PCA methods
• pcaPP-1.9-73 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-0.9-51 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-0.9-4 Functions for Generating Restricted Permutations of Data
• phangorn-2.4.0 Phylogenetic Reconstruction and Analysis
• pheatmap-1.0.12 Pretty Heatmaps
• phylobase-0.8.6 Base Package for Phylogenetic Structures and Comparative Data
• pillar-1.3.1 Coloured Formatting for Columns
• pim-2.0.1 Fit Probabilistic Index Models
• pinfsc50-1.1.0 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-1.0.2 Find Tools Needed to Build R Packages
• pkgconfig-2.0.2 Private Configuration for ‘R’ Packages
• pkgload-1.0.2 Simulate Package Installation and Attach
• pkgmaker-0.27 Development Utilities for R Packages
• plogr-0.2.0 The ‘plog’ C++ Logging Library
• plot3D-1.1.1 Plotting Multi-Dimensional Data
• plot3Drgl-1.0.1 Plotting Multi-Dimensional Data - Using ‘rgl’
• plotly-4.8.0 Create Interactive Web Graphics via ‘plotly.js’
• plotrix-3.7-4 Various Plotting Functions
• pls-2.7-0 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-1.1.14 Polynomial Spline Routines
• polyclip-1.9-1 Polygon Clipping
• polyester-1.18.0 Simulate RNA-seq reads
• polynom-1.3-9 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
• prabclus-2.2-7 Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data
• pracma-2.2.2 Practical Numerical Math Functions
• praise-1.0.0 Praise Users
• preprocessCore-1.44.0 A collection of pre-processing functions
• prettyunits-1.0.2 Pretty, Human Readable Formatting of Quantities
• processx-3.3.0 Execute and Control System Processes
• prodlim-2018.04.18 Product-Limit Estimation for Censored Event History Analysis
• profileModel-0.5-9 Profiling Inference Functions for Various Model Classes
• progress-1.2.0 Terminal Progress Bars
• promises-1.0.1 Abstractions for Promise-Based Asynchronous Programming
• proto-1.0.0 Prototype Object-Based Programming
• proxy-0.4-23 Distance and Similarity Measures
• pryr-0.1.4 Tools for Computing on the Language
• ps-1.3.0 List, Query, Manipulate System Processes
• pscl-1.5.2 Political Science Computational Laboratory
• pspline-1.0-18 Penalized Smoothing Splines
• psych-1.8.12 Procedures for Psychological, Psychometric, and Personality Research
• psychotools-0.5-0 Psychometric Modeling Infrastructure
• pulsar-0.3.5 Parallel Utilities for Lambda Selection along a Regularization Path
• purrr-0.3.1 Functional Programming Tools
• pvclust-2.0-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
• qgraph-1.6.1 Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
• qpdf-1.1 Split, Combine and Compress PDF Files
• qrnn-2.0.3 Quantile Regression Neural Network
• qtl-1.44-9 Tools for Analyzing QTL Experiments
• quadprog-1.5-5 Functions to Solve Quadratic Programming Problems
• quantmod-0.4-13 Quantitative Financial Modelling Framework
• quantreg-5.38 Quantile Regression
• quantsmooth-1.48.0 Quantile smoothing and genomic visualization of array data
• questionr-0.7.0 Functions to Make Surveys Processing Easier
• qvalue-2.14.1 Q-value estimation for false discovery rate control
• qvcalc-0.9-1 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-2.30.0 de novo motif discovery
• rJava-0.9-10 Low-Level R to Java Interface
• randomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and Regression
• randomForestSRC-2.8.0 Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
• ranger-0.11.2 A Fast Implementation of Random Forests
• rappdirs-0.3.1 Application Directories: Determine Where to Save Data, Caches, and Logs
• raster-2.8-19 Geographic Data Analysis and Modeling
• rbenchmark-1.0.0 Benchmarking routine for R
• rcmdcheck-1.3.2 Run ‘R CMD check’ from ‘R’ and Capture Results
• readbitmap-0.1.5 Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF)
• readr-1.3.1 Read Rectangular Text Data
• readxl-1.3.0 Read Excel Files
• recipes-0.1.4 Preprocessing Tools to Create Design Matrices
• refund-0.1-17 Regression with Functional Data
• registry-0.5-1 Infrastructure for R Package Registries
• regress-1.3-15 Gaussian Linear Models with Linear Covariance Structure
• regtools-1.0.1 Regression Tools
• relations-0.6-8 Data Structures and Algorithms for Relations
• relevent-1.0-4 Relational Event Models
• rematch-1.0.1 Match Regular Expressions with a Nicer ‘API’
• remotes-2.0.2 R Package Installation from Remote Repositories, Including ‘GitHub’
• rentrez-1.2.1 ‘Entrez’ in R
• repr-0.19.2 Serializable Representations
• reprex-0.2.1 Prepare Reproducible Example Code via the Clipboard
• reshape-0.8.8 Flexibly Reshape Data
• reshape2-1.4.3 Flexibly Reshape Data: A Reboot of the Reshape Package
• reticulate-1.11.1 Interface to ‘Python’
• rex-1.1.2 Friendly Regular Expressions
• rgdal-1.4-2 Bindings for the ‘Geospatial’ Data Abstraction Library
• rgenoud-5.8-3.0 R Version of GENetic Optimization Using Derivatives
• rgexf-0.15.3 Build, Import and Export GEXF Graph Files
• rgl-0.100.18 3D Visualization Using OpenGL
• rhdf5-2.26.2 HDF5 interface to R
• rio-0.5.16 A Swiss-Army Knife for Data I/O
• ritis-0.7.6 Integrated Taxonomic Information System Client
• rjags-4-8 Bayesian Graphical Models using MCMC
• rjson-0.2.20 JSON for R
• rlang-0.3.1 Functions for Base Types and Core R and ‘Tidyverse’ Features
• rlecuyer-0.3-4 R Interface to RNG with Multiple Streams
• rmarkdown-1.11 Dynamic Documents for R
• rmeta-3.0 Meta-Analysis
• rms-5.1-3 Regression Modeling Strategies
• rncl-0.8.3 An Interface to the Nexus Class Library
• rngtools-1.3.1 Utility Functions for Working with Random Number Generators
• robustbase-0.93-3 Basic Robust Statistics
• rootSolve-1.7 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
• rotl-3.0.7 Interface to the ‘Open Tree of Life’ API
• roxygen2-6.1.1 In-Line Documentation for R
• rpart-4.1-13 Recursive Partitioning and Regression Trees
• rprojroot-1.3-2 Finding Files in Project Subdirectories
• rrcov-1.4-7 Scalable Robust Estimators with High Breakdown Point
• rredlist-0.5.0 ‘IUCN’ Red List Client
• rsconnect-0.8.13 Deployment Interface for R Markdown Documents and Shiny Applications
• rslurm-0.4.0 Submit R Calculations to a Slurm Cluster
• rstudioapi-0.9.0 Safely Access the RStudio API
• rtracklayer-1.42.2 R interface to genome annotation files and the UCSC genome browser
• rvcheck-0.1.3 R/Package Version Check
• rversions-1.0.3 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
• rvest-0.3.2 Easily Harvest (Scrape) Web Pages
• rzmq-0.9.6 R Bindings for ‘ZeroMQ’
• samr-3.0 SAM: Significance Analysis of Microarrays
• sandwich-2.5-0 Robust Covariance Matrix Estimators
• scales-1.0.0 Scale Functions for Visualization
• scatterplot3d-0.3-41 3D Scatter Plot
• scidb-2.0.0 An R Interface to SciDB
• seewave-2.1.0 Sound Analysis and Synthesis
• segmented-0.5-3.0 Regression Models with Break-Points / Change-Points Estimation
• selectr-0.4-1 Translate CSS Selectors to XPath Expressions
• sem-3.1-9 Structural Equation Models
• sendmailR-1.2-1 send email using R
• seqLogo-1.48.0 Sequence logos for DNA sequence alignments
• seqinr-3.4-5 Biological Sequences Retrieval and Analysis
• sessioninfo-1.1.1 R Session Information
• sets-1.0-18 Sets, Generalized Sets, Customizable Sets and Intervals
• sf-0.7-3 Simple Features for R
• sfsmisc-1.1-3 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-1.2.0 Web Application Framework for R
• shinyBS-0.61 Twitter Bootstrap Components for Shiny
• shinyFiles-0.7.2 A Server-Side File System Viewer for Shiny
• shinycssloaders-0.2.0 Add CSS Loading Animations to ‘shiny’ Outputs
• shinydashboard-0.7.1 Create Dashboards with ‘Shiny’
• shinyjs-1.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
• shinythemes-1.1.2 Themes for Shiny
• sigaR-1.30.0 Statistics for Integrative Genomics Analyses in R
• siggenes-1.56.0 Multiple testing using SAM and Efron’s empirical Bayes approaches
• signal-0.7-6 Signal Processing
• slam-0.1-45 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-1.5-3 The Skew-Normal and Related Distributions Such as the Skew-t
• sna-2.4 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-1.32.0 SnpMatrix and XSnpMatrix classes and methods
• solrium-1.0.2 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-1.3-1 Classes and Methods for Spatial Data
• spData-0.3.0 Datasets for Spatial Analysis
• spaMM-2.6.1 Mixed-Effect Models, Particularly Spatial Models
• spam-2.2-2 SPArse Matrix
• sparklyr-1.0.0 R Interface to Apache Spark
• spatial-7.3-11 Functions for Kriging and Point Pattern Analysis
• spatstat-1.58-2 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
• spatstat.data-1.4-0 Datasets for ‘spatstat’
• spatstat.utils-1.13-0 Utility Functions for ‘spatstat’
• spdep-1.0-2 Spatial Dependence: Weighting Schemes, Statistics and Models
• splines built in
• sqldf-0.4-11 Manipulate R Data Frames Using SQL
• ssgraph-1.7 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-0.9.5 Utilities for Start-Up Messages
• statmod-1.4.30 Statistical Modeling
• statnet-2018.10 Software Tools for the Statistical Analysis of Network Data
• statnet.common-4.2.0 Common R Scripts and Utilities Used by the Statnet Project Software
• stats built in
• stats4 built in
• stringdist-0.9.5.1 Approximate String Matching and String Distance Functions
• stringi-1.3.1 Character String Processing Facilities
• stringr-1.4.0 Simple, Consistent Wrappers for Common String Operations
• strucchange-1.5-1 Testing, Monitoring, and Dating Structural Changes
• subplex-1.5-4 Unconstrained Optimization using the Subplex Algorithm
• survey-3.35-1 Analysis of Complex Survey Samples
• survival-2.43-3 Survival Analysis
• survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
• svd-0.4.2 Interfaces to Various State-of-Art SVD and Eigensolvers
• synapseClient 1.14-3
• sys-3.1 Powerful and Reliable Tools for Running System Commands in R
• systemPipeR-1.16.1 systemPipeR: NGS workflow and report generation environment
• tables-0.8.7 Formula-Driven Table Generation
• taxize-0.9.6 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-3.5.2 Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
• testthat-2.0.1 Unit Testing for R
• tibble-2.0.1 Simple Data Frames
• tidygraph-1.1.2 A Tidy API for Graph Manipulation
• tidyr-0.8.3 Easily Tidy Data with ‘spread()’ and ‘gather()’ Functions
• tidyselect-0.2.5 Select from a Set of Strings
• tidytree-0.2.4 A Tidy Tool for Phylogenetic Tree Data Manipulation
• tidyverse-1.2.1 Easily Install and Load the ‘Tidyverse’
• tiff-0.1-5 Read and write TIFF images
• tilingArray-1.60.0 Transcript mapping with high-density oligonucleotide tiling arrays
• timeDate-3043.102 Rmetrics - Chronological and Calendar Objects
• timeSeries-3042.102 Rmetrics - Financial Time Series Objects
• timereg-1.9.3 Flexible Regression Models for Survival Data
• tinytex-0.10 Helper Functions to Install and Maintain ‘TeX Live’, and Compile ‘LaTeX’ Documents
• tkWidgets-1.60.0 R based tk widgets
• tkrplot-0.0-24 TK Rplot
• tm-0.7-6 Text Mining Package
• tmle-1.3.0-2 Targeted Maximum Likelihood Estimation
• tmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distribution
• tools built in
• tree-1.0-39 Classification and Regression Trees
• treeio-1.6.2 Base Classes and Functions for Phylogenetic Tree Input and Output
• triebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’
• trimcluster-0.1-2.1 Cluster Analysis with Trimming
• tripack-1.3-8 Triangulation of Irregularly Spaced Data
• trust-0.1-7 Trust Region Optimization
• tseries-0.10-46 Time Series Analysis and Computational Finance
• tseriesChaos-0.1-13.1 Analysis of Nonlinear Time Series
• tsna-0.2.0 Tools for Temporal Social Network Analysis
• tsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
• 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-0.6-2 Measurement Units for R Vectors
• urca-1.3-0 Unit Root and Cointegration Tests for Time Series Data
• urltools-1.7.2 Vectorised Tools for URL Handling and Parsing
• uroot-2.0-9 Unit Root Tests for Seasonal Time Series
• usethis-1.4.0 Automate Package and Project Setup
• utf8-1.1.4 Unicode Text Processing
• utils built in
• uuid-0.1-2 Tools for generating and handling of UUIDs
• vcd-1.4-4 Visualizing Categorical Data
• vcfR-1.8.0 Manipulate and Visualize VCF Data
• vegan-2.5-4 Community Ecology Package
• venn-1.7 Draw Venn Diagrams
• vioplot-0.3.0 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-2.0.5 Network Visualization using ‘vis.js’ Library
• vsn-3.50.0 Variance stabilization and calibration for microarray data
• waveslim-1.7.5.1 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-0.5.1 Take Screenshots of Web Pages
• whisker-0.3-2 for R, logicless templating
• widgetTools-1.60.0 Creates an interactive tcltk widget
• wikitaxa-0.3.0 Taxonomic Information from ‘Wikipedia’
• withr-2.1.2 Run Code ‘With’ Temporarily Modified Global State
• worrms-0.3.2 World Register of Marine Species (WoRMS) Client
• xfun-0.5 Miscellaneous Functions by ‘Yihui Xie’
• xlsx-0.6.1 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
• xlsxjars-0.6.1 Package required POI jars for the xlsx package
• xml2-1.2.0 Parse XML
• xopen-1.0.0 Open System Files, ‘URLs’, Anything
• xtable-1.8-3 Export Tables to LaTeX or HTML
• xts-0.11-2 eXtensible Time Series
• yaml-2.2.0 Methods to Convert R Data to YAML and Back
• zip-2.0.0 Cross-Platform ‘zip’ Compression
• zlibbioc-1.28.0 An R packaged zlib-1.2.5
• zoo-1.8-4 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)