Known Issues
Package List
- ADGofTest-0.3 Anderson-Darling GoF test
- ALDEx2-1.16.0 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-2.34.0 Processing and Differential Expression Analysis of Agilent microRNA chips
- AlgDesign-1.1-7.3 Algorithmic Experimental Design
- AnnotationDbi-1.46.0 Manipulation of SQLite-based annotations in Bioconductor
- AnnotationFilter-1.8.0 Facilities for Filtering Bioconductor Annotation Resources
- AnnotationForge-1.26.0 Tools for building SQLite-based annotation data packages
- AnnotationHub-2.16.0 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-2.59 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
- BH-1.69.0-1 Boost C++ Header Files
- BSgenome-1.52.0 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-1.8 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-2.44.0 Biobase: Base functions for Bioconductor
- BiocFileCache-1.8.0 Manage Files Across Sessions
- BiocGenerics-0.30.0 S4 generic functions used in Bioconductor
- BiocInstaller 1.8.3
- BiocManager-1.30.4 Access the Bioconductor Project Package Repository
- BiocParallel-1.18.0 Bioconductor facilities for parallel evaluation
- Biostrings-2.52.0 Efficient manipulation of biological strings
- BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
- Bolstad-0.2-40 Functions for Elementary Bayesian Inference
- Bolstad2-1.0-28 Bolstad functions
- BradleyTerry2-1.1-0 Bradley-Terry Models
- Brobdingnag-1.2-6 Very Large Numbers in R
- CGEN-3.20.0 An R package for analysis of case-control studies in genetic epidemiology
- CGHbase-1.44.0 CGHbase: Base functions and classes for arrayCGH data analysis.
- CVST-0.2-2 Fast Cross-Validation via Sequential Testing
- Cairo-1.5-10 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-2.50.0 Category Analysis
- ChIPpeakAnno-3.18.2 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
- ComICS-1.0.4 Computational Methods for Immune Cell-Type Subsets
- CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
- DAAG-1.22.1 Data Analysis and Graphics Data and Functions
- DBI-1.0.0 R Database Interface
- DEGseq-1.38.0 Identify Differentially Expressed Genes from RNA-seq data
- DESeq-1.36.0 Differential gene expression analysis based on the negative binomial distribution
- DESeq2-1.24.0 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-1.58.0 DNA copy number data analysis
- DRR-0.0.3 Dimensionality Reduction via Regression
- DT-0.7 A Wrapper of the JavaScript Library ‘DataTables’
- DTRreg-1.3 DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
- DelayedArray-0.10.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
- DelayedMatrixStats-1.6.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
- Deriv-3.8.5 Symbolic Differentiation
- DiagrammeR-1.0.1 Graph/Network Visualization
- DiffBind-2.12.0 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-1.62.0 Dynamic document tools
- EBImage-4.26.0 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-1.42 Multivariate Exploratory Data Analysis and Data Mining
- Formula-1.2-3 Extended Model Formulas
- GENESIS-2.14.1 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
- GEOquery-2.52.0 Get data from NCBI Gene Expression Omnibus (GEO)
- GGally-1.4.0 Extension to ‘ggplot2’
- GO.db-3.8.2 A set of annotation maps describing the entire Gene Ontology
- GOstats-2.50.0 Tools for manipulating GO and microarrays
- GSA-1.03.1 Gene Set Analysis
- GSEABase-1.46.0 Gene set enrichment data structures and methods
- GSVA-1.32.0 Gene Set Variation Analysis for microarray and RNA-seq data
- GUTS-1.1.1 Fast Calculation of the Likelihood of a Stochastic Survival
Model
- GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
- GWASTools-1.30.0 Tools for Genome Wide Association Studies
- GenSA-1.1.7 Generalized Simulated Annealing
- GeneNet-1.2.13 Modeling and Inferring Gene Networks
- GenomeGraphs-1.44.0 Plotting genomic information from Ensembl
- GenomeInfoDb-1.20.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
- GenomeInfoDbData-1.2.1 Species and taxonomy ID look up tables used by GenomeInfoDb
- GenomicAlignments-1.20.1 Representation and manipulation of short genomic alignments
- GenomicFeatures-1.36.3 Conveniently import and query gene models
- GenomicFiles-1.20.0 Distributed computing by file or by range
- GenomicRanges-1.36.0 Representation and manipulation of genomic intervals
- 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-1.28.0 Plotting data and annotation information along genomic coordinates
- HCsnip 1.2.0
- HDF5Array-1.12.1 HDF5 backend for DelayedArray objects
- HMMcopy-1.26.0 Copy number prediction with correction for GC and mappability bias for HTS data
- HSMMSingleCell-1.4.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
- HWxtest-1.1.9 Exact Tests for Hardy-Weinberg Proportions
- HaploSim-1.8.4 Functions to simulate haplotypes
- 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)’
- IDSpatialStats-0.3.5 Estimate Global Clustering in Infectious Disease
- IHW-1.12.0 Independent Hypothesis Weighting
- IRanges-2.18.1 Foundation of integer range manipulation in Bioconductor
- IRdisplay-0.7.0 ‘Jupyter’ Display Machinery
- ISOcodes-2019.04.22 Selected ISO Codes
- IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
- Iso-0.0-18 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-1.24.0 Client-side REST access to KEGG
- KEGGgraph-1.44.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
- KEGGprofile-1.26.0 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-1.3-1 L-Moments and Quantile Mixtures
- LogicReg-1.5.12 Logic Regression
- LymphoSeq-1.12.0 Analyze high-throughput sequencing of T and B cell receptors
- LymphoSeqDB-0.99.2 LymphoSeq annotation databases
- MASS-7.3-51.4 Support Functions and Datasets for Venables and Ripley’s MASS
- MCMCglmm-2.29 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-4.9-6 Multivariate and Propensity Score Matching with Balance
Optimization
- Matrix-1.2-17 Sparse and Dense Matrix Classes and Methods
- Matrix.utils-0.9.7 Data.frame-Like Operations on Sparse and Dense Matrix Objects
- MatrixEQTL-2.2 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
Operations
- MatrixModels-0.4-1 Modelling with Sparse And Dense Matrices
- Mfuzz-2.44.0 Soft clustering of time series gene expression data
- ModelMetrics-1.2.2 Rapid Calculation of Model Metrics
- MotIV-1.40.0 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-2.28.0 Exploratory analysis and differential expression for RNA-seq data
- OceanView-1.0.4 Visualisation of Oceanographic Data and Model Output
- OrganismDbi-1.26.0 Software to enable the smooth interfacing of different database packages
- PBSddesolve-1.12.4 Solver for Delay Differential Equations
- PFAM.db-3.8.2 A set of protein ID mappings for PFAM
- PICS-2.28.0 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-2.0-2 Polynomials in R
- PresenceAbsence-1.1.9 Presence-Absence Model Evaluation.
- ProtGenerics-1.16.0 S4 generic functions for Bioconductor proteomics infrastructure
- PythonEmbedInR 0.3.29
- 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-2.9.0 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-1.60.0 An interface to the BOOST graph library
- RCircos-1.2.1 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-0.1-16.1 Randomization Inference Tools
- RJSONIO-1.3-1.2 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
- RNASeqPower-1.24.0 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-1.6.0 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-0.15-0 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-1.0.1 Seamless R and C++ Integration
- RcppAnnoy-0.0.12 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest
Neighbors
- RcppArmadillo-0.9.500.2.0 ‘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-4.4.3 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-0.11-0 Update and Manipulate Rd Documentation Objects
- ReportingTools-2.24.0 Tools for making reports in various formats
- Rglpk-0.6-4 R/GNU Linear Programming Kit Interface
- Rgraphviz-2.28.0 Provides plotting capabilities for R graph objects
- Rhdf5lib-1.6.0 hdf5 library as an R package
- Rhpc-0.18-204 Permits *apply() Style Dispatch for ‘HPC’
- RhpcBLASctl-0.18-205 Control the Number of Threads on ‘BLAS’
- Rhtslib-1.16.1 HTSlib high-throughput sequencing library as an R package
- Ringo-1.48.0 R Investigation of ChIP-chip Oligoarrays
- Rlabkey-2.3.0 Data Exchange Between R and ‘LabKey’ Server
- Rmpi-0.6-9 Interface (Wrapper) to MPI (Message-Passing Interface)
- Rook-1.1-1 Rook - a web server interface for R
- Rsamtools-2.0.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
- Rssa-1.0 A Collection of Methods for Singular Spectrum Analysis
- Rsubread-1.34.4 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-0.22.0 Foundation of vector-like and list-like containers in Bioconductor
- SDMTools-1.1-221.1 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-1.18.1 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
- SPIA-2.36.0 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-1.24.1 Data Management of Large-scale Whole-genome Sequence Variant Calls
- SeqVarTools-1.22.0 Tools for variant data
- Seurat-3.1.1 Tools for Single Cell Genomics
- ShortRead-1.42.0 FASTQ input and manipulation
- SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
- SingleCellExperiment-1.6.0 S4 Classes for Single Cell Data
- SnowballC-0.6.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 Library
- SparseM-1.77 Sparse Linear Algebra
- StanHeaders-2.18.1-10 C++ Header Files for Stan
- SummarizedExperiment-1.14.0 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-1.22.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
- TraMineR-2.0-12 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-1.30.1 Annotation of Genetic Variants
- VennDiagram-1.6.20 Generate High-Resolution Venn and Euler Plots
- WikidataR-1.4.0 API Client Library for ‘Wikidata’
- WikipediR-1.5.0 A MediaWiki API Wrapper
- Wrench-1.2.0 Wrench normalization for sparse count data
- 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-0.24.0 Foundation of external vector representation and manipulation in Bioconductor
- abc-2.1 Tools for Approximate Bayesian Computation (ABC)
- abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)
- 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-1.62.0 Methods for Affymetrix Oligonucleotide Arrays
- affycoretools-1.56.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
- affyio-1.54.0 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-0.8-17 Another Multidimensional Analysis Package
- animation-2.6 A Gallery of Animations in Statistics and Utilities to Create
Animations
- annaffy-1.56.0 Annotation tools for Affymetrix biological metadata
- annotate-1.62.0 Annotation for microarrays
- aod-1.3.1 Analysis of Overdispersed Data
- ape-5.3 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
- asnipe-1.1.11 Animal Social Network Inference and Permutations for Ecologists
- assertthat-0.2.1 Easy Pre and Post Assertions
- audio-0.1-6 Audio Interface for R
- aws.ec2metadata-0.1.6 Get EC2 Instance Metadata
- aws.s3-0.3.12 ‘AWS S3’ Client Package
- aws.signature-0.4.4 Amazon Web Services Request Signatures
- backports-1.1.4 Reimplementations of Functions Introduced Since R-3.0.0
- bartMachine-1.2.4.2 Bayesian Additive Regression Trees
- bartMachineJARs-1.1 bartMachine JARs
- base built in
- base64-2.0 Base64 Encoder and Decoder
- base64enc-0.1-3 Tools for base64 encoding
- base64url-1.4 Fast and URL-Safe Base64 Encoder and Decoder
- batchtools-0.9.11 Tools for Computation on Batch Systems
- baySeq-2.18.0 Empirical Bayesian analysis of patterns of differential expression in count data
- bayesm-3.1-1 Bayesian Inference for Marketing/Micro-Econometrics
- bayesplot-1.7.0 Plotting for Bayesian Models
- 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-2.40.1 Interface to BioMart databases (i.e. Ensembl)
- biovizBase-1.32.0 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-0.9.0 Interface to Bold Systems API
- boot-1.3-23 Bootstrap Functions (Originally by Angelo Canty for S)
- bootstrap-2019.6 Functions for the Book “An Introduction to the Bootstrap”
- breakaway-3.0 Species Richness Estimation and Modeling
- brew-1.0-6 Templating Framework for Report Generation
- brglm-0.6.2 Bias Reduction in Binomial-Response Generalized Linear Models
- bridgedist-0.1.0 An Implementation of the Bridge Distribution with Logit-Link as
in Wang and Louis (2003)
- bridgesampling-0.6-0 Bridge Sampling for Marginal Likelihoods and Bayes Factors
- broom-0.5.2 Convert Statistical Analysis Objects into Tidy Tibbles
- bst-0.3-17 Gradient Boosting
- bumphunter-1.26.0 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-3.3.0 Call R from R
- car-3.0-3 Companion to Applied Regression
- carData-3.0-2 Companion to Applied Regression Data Sets
- caret-6.0-84 Classification and Regression Training
- catdata-1.2.1 Categorical Data
- cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
- cgdsr-1.3.0 R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
- cghFLasso-0.2-1 Detecting hot spot on CGH array data with fused lasso<U+000a>regression.
- checkmate-1.9.4 Fast and Versatile Argument Checks
- chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
- chipseq-1.34.0 chipseq: A package for analyzing chipseq data
- chron-2.3-53 Chronological Objects which can Handle Dates and Times
- circlize-0.4.6 Circular Visualization
- circular-0.4-93 Circular Statistics
- clValid-0.6-6 Validation of Clustering Results
- class-7.3-15 Functions for Classification
- classInt-0.3-3 Choose Univariate Class Intervals
- cli-1.1.0 Helpers for Developing Command Line Interfaces
- clipr-0.6.0 Read and Write from the System Clipboard
- clisymbols-1.2.0 Unicode Symbols at the R Prompt
- clue-0.3-57 Cluster Ensembles
- cluster-2.1.0 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et
al.
- clusterGeneration-1.3.4 Random Cluster Generation (with Specified Degree of Separation)
- clusterRepro-0.9 Reproducibility of Gene Expression Clusters
- clustree-0.4.0 Visualise Clusterings at Different Resolutions
- coda-0.19-3 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-1.4-1 A Toolbox for Manipulating and Assessing Colors and Palettes
- colourpicker-1.0 A Colour Picker Tool for Shiny and for Selecting Colours in
Plots
- combinat-0.0-8 combinatorics utilities
- commonmark-1.7 High Performance CommonMark and Github Markdown Rendering in R
- compare-0.2-6 Comparing Objects for Differences
- compositions-1.40-2 Compositional Data Analysis
- config-0.3 Manage Environment Specific Configuration Values
- copula-0.999-19.1 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-2.2-14 Mixed Effects Cox Models
- crayon-1.3.4 Colored Terminal Output
- crosstalk-1.0.0 Inter-Widget Interactivity for HTML Widgets
- crul-0.8.0 HTTP Client
- csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
- cubature-2.0.3 Adaptive Multivariate Integration over Hypercubes
- cummeRbund-2.26.0 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-1.6.0 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
- dada2-1.12.1 Accurate, high-resolution sample inference from amplicon sequencing data
- data.table-1.12.2 Extension of
data.frame
- datasets built in
- dbplyr-1.4.2 A ‘dplyr’ Back End for Databases
- ddalpha-1.3.9 Depth-Based Classification and Calculation of Data Depth
- deSolve-1.23 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-0.1-22 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
- dendextend-1.12.0 Extending ‘dendrogram’ Functionality in R
- derfinder-1.18.3 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
- derfinderHelper-1.18.1 derfinder helper package
- desc-1.2.0 Manipulate DESCRIPTION Files
- descr-1.1.4 Descriptive Statistics
- devtools-2.1.0 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
- dials-0.0.2 Tools for Creating Tuning Parameter Values
- diamonds-1.0-5 Analysis and sampling grids from diamond partitions
- dichromat-2.0-0 Color Schemes for Dichromats
- digest-0.6.20 Create Compact Hash Digests of R Objects
- dimRed-0.2.3 A Framework for Dimensionality Reduction
- diptest-0.75-7 Hartigan’s Dip Test Statistic for Unimodality - Corrected
- dismo-1.1-4 Species Distribution Modeling
- distillery-1.0-6 Method Functions for Confidence Intervals and to Distill
Information from an Object
- distr-2.8.0 Object Oriented Implementation of Distributions
- distrEx-2.8.0 Extensions of Package ‘distr’
- diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis
Package
- doBy-4.6-2 Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
- 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-0.8.3 A Grammar of Data Manipulation
- dqrng-0.2.1 Fast Pseudo Random Number Generators
- 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
- dygraphs-1.1.1.6 Interface to ‘Dygraphs’ Interactive Time Series Charting Library
- dynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering
Dendrograms
- e1071-1.7-2 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
- edgeR-3.26.5 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-0.2.0.1 Tools for Working with …
- emulator-1.2-20 Bayesian Emulation of Computer Programs
- energy-1.7-6 E-Statistics: Multivariate Inference via the Energy of Data
- ensembldb-2.8.0 Utilities to create and use Ensembl-based annotation databases
- ergm-3.10.4 Fit, Simulate and Diagnose Exponential-Family Models for
Networks
- ergm.count-3.4.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
- evaluate-0.14 Parsing and Evaluation Tools that Provide More Details than the
Default
- expm-0.999-4 Matrix Exponential, Log, ‘etc’
- expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
- extRemes-2.0-10 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-1.2-2 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-1.30.0 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-0.3.3 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-9.8-3 Tools for Spatial Data
- filehash-2.4-2 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-3.22.0 Clustering for Flow Cytometry
- flowCore-1.50.0 flowCore: Basic structures for flow cytometry data
- flowStats-3.42.0 Statistical methods for the analysis of flow cytometry data
- flowViz-1.48.0 Visualization for flow cytometry
- flowWorkspace-3.32.0 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
- forecast-8.7 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-1.7 Format R Code Automatically
- fossil-0.3.7 Palaeoecological and Palaeogeographical Analysis Tools
- fpc-2.2-3 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-1.3.1 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-1.14.0 Unified Parallel and Distributed Processing in R for Everyone
- future.apply-1.3.0 Apply Function to Elements in Parallel using Futures
- gage-2.34.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
- gam-1.16.1 Generalized Additive Models
- gamlss-5.1-4 Generalised Additive Models for Location Scale and Shape
- gamlss.data-5.1-4 GAMLSS Data
- gamlss.dist-5.1-4 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-1.2.1 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-2.56.0 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-1.20.0 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-2.0.6.2 Analysis of Evolutionary Diversification
- geneLenDataBase-1.20.0 Lengths of mRNA transcripts for a number of genomes
- genefilter-1.66.0 genefilter: methods for filtering genes from high-throughput experiments
- geneplotter-1.62.0 Graphics related functions for Bioconductor
- generics-0.0.2 Common S3 Generics not Provided by Base R Methods Related to
Model Fitting
- genoset-1.40.0 A RangedSummarizedExperiment with methods for copy number analysis
- geometry-0.4.1.1 Mesh Generation and Surface Tessellation
- getopt-1.20.3 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-1.32.0 Visualization tools for genomic data
- ggforce-0.2.2 Accelerating ‘ggplot2’
- ggm-2.3 Functions for graphical Markov models
- ggplot2-3.2.0 Create Elegant Data Visualisations Using the Grammar of Graphics
- ggraph-1.0.2 An Implementation of Grammar of Graphics for Graphs and Networks
- ggrepel-0.8.1 Automatically Position Non-Overlapping Text Labels with
‘ggplot2’
- ggridges-0.5.1 Ridgeline Plots in ‘ggplot2’
- ggthemes-4.2.0 Extra Themes, Scales and Geoms for ‘ggplot2’
- ggtree-1.16.3 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-0.26.1 Provides Access to Git Repositories
- glasso-1.10 Graphical Lasso: Estimation of Gaussian Graphical Models
- gllvm-1.1.3 Generalized Linear Latent Variable Models
- glmmML-1.1.0 Generalized Linear Models with Clustering
- glmmTMB-0.2.3 Generalized Linear Mixed Models using Template Model Builder
- glmnet-2.0-18 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-1.3.1 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-1.36.0 Gene Ontology analyser for RNA-seq and other length biased data
- gower-0.2.1 Gower’s Distance
- gplots-3.0.1.1 Various R Programming Tools for Plotting Data
- grDevices built in
- graph-1.62.0 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
- grr-0.9.5 Alternative Implementations of Base R Functions
- gsalib-2.1 Utility Functions For GATK
- gsl-2.1-6 Wrapper for the Gnu Scientific Library
- gsubfn-0.7 Utilities for Strings and Function Arguments
- gsw-1.0-5 Gibbs Sea Water Functions
- gtable-0.3.0 Arrange ‘Grobs’ in Tables
- gtools-3.8.1 Various R Programming Tools
- h2o-3.24.0.5 R Interface for ‘H2O’
- 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-2.1.1 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
- hdf5r-1.2.0 Interface to the ‘HDF5’ Binary Data Format
- heatmap3-1.1.6 An Improved Heatmap Package
- hexbin-1.27.3 Hexagonal Binning Routines
- hgu133plus2.db-3.2.3 Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2)
- highr-0.8 Syntax Highlighting for R Source Code
- hms-0.4.2 Pretty Time of Day
- hopach-2.44.0 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-1.5.1 HTTP and WebSocket Server Library
- httr-1.4.0 Tools for Working with URLs and HTTP
- huge-1.3.2 High-Dimensional Undirected Graph Estimation
- hunspell-3.0 High-Performance Stemmer, Tokenizer, and Spell Checker
- hwriter-1.3.2 HTML Writer - Outputs R objects in HTML format
- ica-1.0-2 Independent Component Analysis
- idr-1.2 Irreproducible discovery rate
- igraph-1.2.4.1 Network Analysis and Visualization
- igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
- illuminaio-0.26.0 Parsing Illumina Microarray Output Files
- imager-0.41.2 Image Processing Library Based on ‘CImg’
- impute-1.58.0 impute: Imputation for microarray data
- ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
- infer-0.4.0.1 Tidy Statistical Inference
- inferference-1.0.0 Methods for Causal Inference with Interference
- influenceR-0.1.0 Software Tools to Quantify Structural Importance of Nodes in a
Network
- infotheo-1.2.0 Information-Theoretic Measures
- ini-0.3.1 Read and Write ‘.ini’ Files
- inline-0.3.15 Functions to Inline C, C++, Fortran Function Calls from R
- interactiveDisplayBase-1.22.0 Base package for enabling powerful shiny web displays of Bioconductor objects
- interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
- inum-1.0-1 Interval and Enum-Type Representation of Vectors
- ipred-0.9-9 Improved Predictors
- irace-3.3 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
- itertools-0.1-3 Iterator Tools
- its-1.1.8 Irregular Time Series
- janeaustenr-0.1.5 Jane Austen’s Complete Novels
- jomo-2.6-8 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
- kinship2-1.8.4 Pedigree Functions
- klaR-0.6-14 Classification and Visualization
- knitr-1.23 A General-Purpose Package for Dynamic Report Generation in R
- kohonen-3.0.8 Supervised and Unsupervised Self-Organising Maps
- ks-1.11.5 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-2.2.1 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 Scheduling Functions to Execute Later with Event
Loops
- 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-0.6-4 Latent Variable Analysis
- lazy-1.2-16 Lazy Learning for Local Regression
- lazyeval-0.2.2 Lazy (Non-Standard) Evaluation
- leaps-3.0 Regression Subset Selection
- leiden-0.3.1 R Implementation of Leiden Clustering Algorithm
- 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-3.40.2 Linear Models for Microarray Data
- lintr-1.0.3 A ‘Linter’ for R Code
- liquidSVM-1.2.2.1 A Fast and Versatile SVM Package
- listenv-0.7.0 Environments Behaving (Almost) as Lists
- lme4-1.1-21 Linear Mixed-Effects Models using ‘Eigen’ and S4
- lmtest-0.9-37 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-2.1.13 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
- loo-2.1.0 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
- lpSolve-5.6.13.1 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
- lpridge-1.0-8 Local Polynomial (Ridge) Regression
- lpsymphony-1.12.0 Symphony integer linear programming solver in R
- lqa-1.0-3 Penalized Likelihood Inference for GLMs
- 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-2.36.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
- maSigPro-1.56.0 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-1.0 Render Markdown with the C Library ‘Sundown’
- marray-1.62.0 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-1.3-6 Maximum Likelihood Estimation and Related Tools
- mboost-2.9-1 Model-Based Boosting
- mclust-5.4.4 Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
- mcmc-0.9-6 Markov Chain Monte Carlo
- mediation-4.4.7 Causal Mediation Analysis
- memoise-1.1.0 Memoisation of Functions
- memuse-4.0-0 Memory Estimation Utilities
- metagenomeSeq-1.26.0 Statistical analysis for sparse high-throughput sequencing
- metap-1.1 Meta-Analysis of Significance Values
- methods built in
- methylumi-2.30.0 Handle Illumina methylation data
- mets-1.2.5 Analysis of Multivariate Event Times
- mgcv-1.8-28 Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
- mi-1.0 Missing Data Imputation and Model Checking
- mice-3.5.0 Multivariate Imputation by Chained Equations
- mime-0.7 Map Filenames to MIME Types
- minfi-1.30.0 Analyze Illumina Infinium DNA methylation arrays
- miniUI-0.1.1.1 Shiny UI Widgets for Small Screens
- minpack.lm-1.2-1 R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
- minqa-1.2.4 Derivative-free optimization algorithms by quadratic<U+000a>approximation
- misc3d-0.8-4 Miscellaneous 3D Plots
- miscTools-0.6-22 Miscellaneous Tools and Utilities
- missForest-1.4 Nonparametric Missing Value Imputation using Random Forest
- mitml-0.3-7 Tools for Multiple Imputation in Multilevel Modeling
- mitools-2.4 Tools for Multiple Imputation of Missing Data
- mixOmics-6.8.0 Omics Data Integration Project
- mixtools-1.1.0 Tools for Analyzing Finite Mixture Models
- mlbench-2.1-1 Machine Learning Benchmark Problems
- mlegp-3.1.7 Maximum Likelihood Estimates of Gaussian Processes
- mlogit-0.4-2 Multinomial Logit Models
- mlr-2.14.0 Machine Learning in R
- mltools-0.3.5 Machine Learning Tools
- 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
- monocle3 0.1.3
- mpath-0.3-15 Regularized Linear Models
- msa-1.16.0 Multiple Sequence Alignment
- msm-1.6.7 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-2.40.0 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-1.0-11 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-2.30.1 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
- ndtv-0.13.0 Network Dynamic Temporal Visualizations
- network-1.15 Classes for Relational Data
- networkDynamic-0.10.0 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-3.1-140 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-1.3-0 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-2016.8-1.1 Accurate Numerical Derivatives
- nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
- oce-1.1-1 Analysis of Oceanographic Data
- oddsratio-2.0.0 Odds Ratio Calculation for GAM(M)s & GLM(M)s
- oligoClasses-1.46.0 Classes for high-throughput arrays supported by oligo and crlmm
- openCyto-1.22.2 Hierarchical Gating Pipeline for flow cytometry data
- openssl-1.4 Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
- openxlsx-4.1.0.1 Read, Write and Edit XLSX Files
- optmatch-0.9-10 Functions for Optimal Matching
- optparse-1.6.2 Command Line Option Parser
- ordinal-2019.4-25 Regression Models for Ordinal Data
- org.Hs.eg.db-3.8.2 Genome wide annotation for Human
- pROC-1.15.0 Display and Analyze ROC Curves
- pack-0.1-1 Convert values to/from raw vectors
- packrat-0.5.0 A Dependency Management System for Projects and their R Package
Dependencies
- pan-1.6 Multiple Imputation for Multivariate Panel or Clustered Data
- parallelMap-1.4 Unified Interface to Parallelization Back-Ends
- parsedate-1.2.0 Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formats
- parsnip-0.0.2 A Common API to Modeling and Analysis Functions
- partools-1.1.6 Tools for the ‘Parallel’ Package
- party-1.3-3 A Laboratory for Recursive Partytioning
- partykit-1.2-4 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
- pbmcapply-1.5.0 Tracking the Progress of Mc*pply with Progress Bar
- pbs-1.1 Periodic B Splines
- pcaMethods-1.76.0 A collection of PCA methods
- pcaPP-1.9-73 Robust PCA by Projection Pursuit
- pdftools-2.2 Text Extraction, Rendering and Converting of PDF Documents
- pdist-1.2 Partitioned Distance Function
- pedigree-1.4 Pedigree functions
- pedigreemm-0.3-3 Pedigree-based mixed-effects models
- penalized-0.9-51 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
- peperr-1.1-7.1 Parallelised Estimation of Prediction Error
- perm-1.0-0.0 Exact or Asymptotic permutation tests
- permute-0.9-5 Functions for Generating Restricted Permutations of Data
- phangorn-2.5.5 Phylogenetic Reconstruction and Analysis
- pheatmap-1.0.12 Pretty Heatmaps
- phylobase-0.8.6 Base Package for Phylogenetic Structures and Comparative Data
- pillar-1.4.2 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-1.0.3 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-4.9.0 Create Interactive Web Graphics via ‘plotly.js’
- plotrix-3.7-6 Various Plotting Functions
- pls-2.7-1 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-1.1.15 Polynomial Spline Routines
- polyclip-1.10-0 Polygon Clipping
- polyester-1.20.0 Simulate RNA-seq reads
- polynom-1.4-0 A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulations
- prabclus-2.3-1 Functions for Clustering and Testing of Presence-Absence,
Abundance and Multilocus Genetic Data
- pracma-2.2.5 Practical Numerical Math Functions
- praise-1.0.0 Praise Users
- preprocessCore-1.46.0 A collection of pre-processing functions
- prettyunits-1.0.2 Pretty, Human Readable Formatting of Quantities
- processx-3.4.0 Execute and Control System Processes
- prodlim-2018.04.18 Product-Limit Estimation for Censored Event History Analysis
- profileModel-0.6.0 Profiling Inference Functions for Various Model Classes
- progress-1.2.2 Terminal Progress Bars
- promises-1.0.1 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-0.3.2 Functional Programming Tools
- pvclust-2.0-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
- qgraph-1.6.3 Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
- qpdf-1.1 Split, Combine and Compress PDF Files
- qrnn-2.0.4 Quantile Regression Neural Network
- qtl-1.44-9 Tools for Analyzing QTL Experiments
- quadprog-1.5-7 Functions to Solve Quadratic Programming Problems
- quantmod-0.4-15 Quantitative Financial Modelling Framework
- quantreg-5.41 Quantile Regression
- quantsmooth-1.50.0 Quantile smoothing and genomic visualization of array data
- questionr-0.7.0 Functions to Make Surveys Processing Easier
- qvalue-2.16.0 Q-value estimation for false discovery rate control
- qvcalc-1.0.0 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-2.32.0 de novo motif discovery
- rJava-0.9-11 Low-Level R to Java Interface
- randomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and
Regression
- randomForestSRC-2.9.0 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-2.9-5 Geographic Data Analysis and Modeling
- rbenchmark-1.0.0 Benchmarking routine for R
- rcmdcheck-1.3.3 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-1.3.1 Read Excel Files
- recipes-0.1.6 Preprocessing Tools to Create Design Matrices
- refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from
‘Ensembl’ and ‘UCSC’ Genome Browsers
- refund-0.1-17 Regression with Functional Data
- regioneR-1.16.2 Association analysis of genomic regions based on permutation tests
- 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 and Classification 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’
- rematch2-2.0.1 Tidy Output from Regular Expression Matching
- remotes-2.1.0 R Package Installation from Remote Repositories, Including
‘GitHub’
- rentrez-1.2.2 ‘Entrez’ in R
- repr-1.0.1 Serializable Representations
- reprex-0.3.0 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-1.12 Interface to ‘Python’
- rex-1.1.2 Friendly Regular Expressions
- rgdal-1.4-4 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-0.100.24 3D Visualization Using OpenGL
- rhdf5-2.28.0 R Interface to HDF5
- 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-0.4.0 Functions for Base Types and Core R and ‘Tidyverse’ Features
- rlecuyer-0.3-4 R Interface to RNG with Multiple Streams
- rmarkdown-1.13 Dynamic Documents for R
- rmeta-3.0 Meta-Analysis
- rms-5.1-3.1 Regression Modeling Strategies
- rncl-0.8.3 An Interface to the Nexus Class Library
- rngtools-1.4 Utility Functions for Working with Random Number Generators
- robustbase-0.93-5 Basic Robust Statistics
- rootSolve-1.7 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
- rotl-3.0.9 Interface to the ‘Open Tree of Life’ API
- roxygen2-6.1.1 In-Line Documentation for R
- rpart-4.1-15 Recursive Partitioning and Regression Trees
- rprojroot-1.3-2 Finding Files in Project Subdirectories
- rrcov-1.4-7 Scalable Robust Estimators with High Breakdown Point
- rredlist-0.5.0 ‘IUCN’ Red List Client
- rsample-0.0.4 General Resampling Infrastructure
- rsconnect-0.8.13 Deployment Interface for R Markdown Documents and Shiny
Applications
- rslurm-0.4.0 Submit R Calculations to a Slurm Cluster
- rstan-2.18.2 R Interface to Stan
- rstanarm-2.18.2 Bayesian Applied Regression Modeling via Stan
- rstantools-1.5.1 Tools for Developing R Packages Interfacing with ‘Stan’
- rstudioapi-0.10 Safely Access the RStudio API
- rsvd-1.0.2 Randomized Singular Value Decomposition
- rtracklayer-1.44.0 R interface to genome annotation files and the UCSC genome browser
- rvcheck-0.1.3 R/Package Version Check
- rversions-2.0.0 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
- rvest-0.3.4 Easily Harvest (Scrape) Web Pages
- rzmq-0.9.6 R Bindings for ‘ZeroMQ’
- samr-3.0 SAM: Significance Analysis of Microarrays
- sandwich-2.5-1 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
- scrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
- sctransform-0.2.0 Variance Stabilizing Transformations for Single Cell UMI Data
- seewave-2.1.3 Sound Analysis and Synthesis
- segmented-1.0-0 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-1.50.0 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-0.7-6 Simple Features for R
- sfsmisc-1.1-4 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-1.3.2 Web Application Framework for R
- shinyBS-0.61 Twitter Bootstrap Components for Shiny
- shinyFiles-0.7.3 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
- shinystan-2.5.0 Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
- shinythemes-1.1.2 Themes for Shiny
- sigaR-1.32.0 Statistics for Integrative Genomics Analyses in R
- siggenes-1.58.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
- signal-0.7-6 Signal Processing
- sitmo-2.0.1 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header
Files
- slam-0.1-45 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-1.5-4 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-1.34.0 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-3.0.0 Mixed-Effect Models, Particularly Spatial Models
- spam-2.2-2 SPArse Matrix
- sparklyr-1.0.2 R Interface to Apache Spark
- spatial-7.3-11 Functions for Kriging and Point Pattern Analysis
- spatstat-1.60-1 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-1.1-2 Spatial Dependence: Weighting Schemes, Statistics
- speedglm-0.3-2 Fitting Linear and Generalized Linear Models to Large Data Sets
- splines built in
- sqldf-0.4-11 Manipulate R Data Frames Using SQL
- ssgraph-1.8 Bayesian Graphical Estimation using Spike-and-Slab Priors
- stabledist-0.7-1 Stable Distribution Functions
- stabs-0.6-3 Stability Selection with Error Control
- startupmsg-0.9.6 Utilities for Start-Up Messages
- statmod-1.4.32 Statistical Modeling
- statnet-2019.6 Software Tools for the Statistical Analysis of Network Data
- statnet.common-4.3.0 Common R Scripts and Utilities Used by the Statnet Project
Software
- stats built in
- stats4 built in
- stopwords-0.9.0 Multilingual Stopword Lists
- stringdist-0.9.5.2 Approximate String Matching and String Distance Functions
- stringi-1.4.3 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-3.36 Analysis of Complex Survey Samples
- survival-2.44-1.1 Survival Analysis
- survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
- svd-0.4.3 Interfaces to Various State-of-Art SVD and Eigensolvers
- synapser 0.6.56
- sys-3.2 Powerful and Reliable Tools for Running System Commands in R
- systemPipeR-1.18.2 systemPipeR: NGS workflow and report generation environment
- tables-0.8.8 Formula-Driven Table Generation
- taxize-0.9.8 Taxonomic Information from Around the Web
- tclust-1.4-1 Robust Trimmed Clustering
- tensor-1.5 Tensor product of arrays
- tensorA-0.36.1 Advanced Tensor Arithmetic with Named Indices
- tergm-3.6.1 Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
- testthat-2.1.1 Unit Testing for R
- threejs-0.3.1 Interactive 3D Scatter Plots, Networks and Globes
- tibble-2.1.3 Simple Data Frames
- tidygraph-1.1.2 A Tidy API for Graph Manipulation
- tidymodels-0.0.2 Easily Install and Load the ‘Tidymodels’ Packages
- tidyposterior-0.0.2 Bayesian Analysis to Compare Models using Resampling Statistics
- tidypredict-0.3.0 Run Predictions Inside the Database
- tidyr-0.8.3 Tidy Messy Data
- tidyselect-0.2.5 Select from a Set of Strings
- tidytext-0.2.1 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Tools
- 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-1.62.0 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-0.14 Helper Functions to Install and Maintain ‘TeX Live’, and Compile
‘LaTeX’ Documents
- tkWidgets-1.62.0 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
- tokenizers-0.2.1 Fast, Consistent Tokenization of Natural Language Text
- tools built in
- tree-1.0-40 Classification and Regression Trees
- treeio-1.8.1 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-0.10-47 Time Series Analysis and Computational Finance
- tseriesChaos-0.1-13.1 Analysis of Nonlinear Time Series
- tsna-0.3.0 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-0.6-3 Measurement Units for R Vectors
- urca-1.3-0 Unit Root and Cointegration Tests for Time Series Data
- urltools-1.7.3 Vectorised Tools for URL Handling and Parsing
- uroot-2.0-9.1 Unit Root Tests for Seasonal Time Series
- usethis-1.5.0 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
- uwot-0.1.3 The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
- vcd-1.4-4 Visualizing Categorical Data
- vcfR-1.8.0 Manipulate and Visualize VCF Data
- vctrs-0.1.0 Vector Helpers
- vegan-2.5-5 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-2.0.6 Network Visualization using ‘vis.js’ Library
- vsn-3.52.0 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-1.62.0 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
- xCell 1.2
- xfun-0.7 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-1.8-4 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
- yardstick-0.0.3 Tidy Characterizations of Model Performance
- zeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignment
- zip-2.0.2 Cross-Platform ‘zip’ Compression
- zlibbioc-1.30.0 An R packaged zlib-1.2.5
- zoo-1.8-5 S3 Infrastructure for Regular and Irregular Time Series (Z’s
Ordered Observations)