fhR-4.1.2-foss-2020b
Edit this Page via GitHub Comment by Filing an Issue Have Questions? Ask them here.The fhR module contains libraries that have been requested by Hutch users. The Fred Hutch module inherits the modules from the base R module that is maintained by the EasyBuild community. Hutch users should use the fh versions of R.
Known Issues
- None
Package List
- ADGofTest-0.3 Anderson-Darling GoF test
- AICcmodavg-2.3-1 Model Selection and Multimodel Inference Based on (Q)AIC(c)
- ALDEx2-1.26.0 Analysis Of Differential Abundance Taking Sample Variation Into Account
- ALL-1.36.0 A data package
- ASCAT 2.5.2
- AUC-0.3.0 Threshold independent performance measures for probabilistic classifiers.
- AgiMicroRna-2.44.0 Processing and Differential Expression Analysis of Agilent microRNA chips
- AlgDesign-1.2.0 Algorithmic Experimental Design
- AnalyzeFMRI-1.1-24 Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format
- AnnotationDbi-1.56.2 Manipulation of SQLite-based annotations in Bioconductor
- AnnotationFilter-1.18.0 Facilities for Filtering Bioconductor Annotation Resources
- AnnotationForge-1.36.0 Tools for building SQLite-based annotation data packages
- AnnotationHub-3.2.0 Client to access AnnotationHub resources
- ArchR 1.0.1
- BB-2019.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
- BBmisc-1.11 Miscellaneous Helper Functions for B. Bischl
- BCEE-1.3.0 The Bayesian Causal Effect Estimation Algorithm
- BDgraph-2.64 Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
- BH-1.75.0-0 Boost C++ Header Files
- BIGL-1.6.5 Biochemically Intuitive Generalized Loewe Model
- BMA-3.18.15 Bayesian Model Averaging
- BSgenome-1.62.0 Software infrastructure for efficient representation of full genomes and their SNPs
- BSgenome.Hsapiens.UCSC.hg19-1.4.3 Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)
- BatchJobs-1.8 Batch Computing with R
- BayesPen-1.0 Bayesian Penalized Credible Regions
- BayesianTools-0.1.7 General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
- Bhat-0.9-10 General likelihood exploration
- BiasedUrn-1.07 Biased Urn Model Distributions
- Biobase-2.54.0 Biobase: Base functions for Bioconductor
- BiocFileCache-2.2.0 Manage Files Across Sessions
- BiocGenerics-0.40.0 S4 generic functions used in Bioconductor
- BiocIO-1.4.0 Standard Input and Output for Bioconductor Packages
- BiocManager-1.30.16 Access the Bioconductor Project Package Repository
- BiocNeighbors-1.12.0 Nearest Neighbor Detection for Bioconductor Packages
- BiocParallel-1.28.1 Bioconductor facilities for parallel evaluation
- BiocSingular-1.10.0 Singular Value Decomposition for Bioconductor Packages
- BiocStyle-2.22.0 Standard styles for vignettes and other Bioconductor documents
- BiocVersion-3.14.0 Set the appropriate version of Bioconductor packages
- Biostrings-2.62.0 Efficient manipulation of biological strings
- BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
- Bolstad-0.2-41 Functions for Elementary Bayesian Inference
- Bolstad2-1.0-28 Bolstad functions
- Boruta-7.0.0 Wrapper Algorithm for All Relevant Feature Selection
- BradleyTerry2-1.1-2 Bradley-Terry Models
- Brobdingnag-1.2-6 Very Large Numbers in R
- CATALYST-1.18.0 Cytometry dATa anALYSis Tools
- CBPS-0.22 Covariate Balancing Propensity Score
- CGHbase-1.54.0 CGHbase: Base functions and classes for arrayCGH data analysis.
- CLONETv2-2.2.1 Clonality Estimates in Tumor
- CMA-1.52.0 Synthesis of microarray-based classification
- CNEr-1.30.0 CNE Detection and Visualization
- COMPASS-1.32.0 Combinatorial Polyfunctionality Analysis of Single Cells
- CVST-0.2-2 Fast Cross-Validation via Sequential Testing
- Cairo-1.5-12.2 R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output
- Category-2.60.0 Category Analysis
- ChIPpeakAnno-3.28.0 Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
- ChIPseeker-1.30.2 ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
- ComICS-1.0.4 Computational Methods for Immune Cell-Type Subsets
- CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
- ComplexHeatmap-2.10.0 Make Complex Heatmaps
- ConsensusClusterPlus-1.58.0 ConsensusClusterPlus
- CovSel-1.2.1 Model-Free Covariate Selection
- CytoML-2.6.0 A GatingML Interface for Cross Platform Cytometry Data Sharing
- DAAG-1.24 Data Analysis and Graphics Data and Functions
- DBI-1.1.1 R Database Interface
- DECIPHER-2.22.0 Tools for curating, analyzing, and manipulating biological sequences
- DEGseq-1.48.0 Identify Differentially Expressed Genes from RNA-seq data
- DESeq2-1.34.0 Differential gene expression analysis based on the negative binomial distribution
- DEoptim-2.2-6 Global Optimization by Differential Evolution
- DEoptimR-1.0-9 Differential Evolution Optimization in Pure R
- DHARMa-0.4.4 Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
- DMCfun-2.0.2 Diffusion Model of Conflict (DMC) in Reaction Time Tasks
- DNAcopy-1.68.0 DNA copy number data analysis
- DO.db-2.9 A set of annotation maps describing the entire Disease Ontology
- DOSE-3.20.1 Disease Ontology Semantic and Enrichment analysis
- DOT-0.1 Render and Export DOT Graphs in R
- DRR-0.0.4 Dimensionality Reduction via Regression
- DT-0.19 A Wrapper of the JavaScript Library ‘DataTables’
- DTRreg-1.7 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
- DelayedArray-0.20.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
- DelayedMatrixStats-1.16.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
- Deriv-4.1.3 Symbolic Differentiation
- DescTools-0.99.43 Tools for Descriptive Statistics
- DiagrammeR-1.0.6.1 Graph/Network Visualization
- DiceDesign-1.9 Designs of Computer Experiments
- DiceKriging-1.6.0 Kriging Methods for Computer Experiments
- DiffBind-3.4.0 Differential Binding Analysis of ChIP-Seq Peak Data
- DirichletMultinomial-1.36.0 Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
- DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
- DistributionUtils-0.6-0 Distribution Utilities
- DynDoc-1.72.0 Dynamic document tools
- EBImage-4.36.0 Image processing and analysis toolbox for R
- ENMeval-2.0.1 Automated Tuning and Evaluations of Ecological Niche Models
- EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
- EnvStats-2.4.0 Package for Environmental Statistics, Including US EPA Guidance
- EpiModel-2.2.0 Mathematical Modeling of Infectious Disease Dynamics
- Exact-3.0 Unconditional Exact Test
- FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
- FME-1.3.6.2 A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis
- FNN-1.1.3 Fast Nearest Neighbor Search Algorithms and Applications
- FactoMineR-2.4 Multivariate Exploratory Data Analysis and Data Mining
- FlowSOM-2.2.0 Using self-organizing maps for visualization and interpretation of cytometry data
- Formula-1.2-4 Extended Model Formulas
- GENESIS-2.24.0 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
- GEOquery-2.62.1 Get data from NCBI Gene Expression Omnibus (GEO)
- GGally-2.1.2 Extension to ‘ggplot2’
- GO.db-3.14.0 A set of annotation maps describing the entire Gene Ontology
- GOSemSim-2.20.0 GO-terms Semantic Similarity Measures
- GOstats-2.60.0 Tools for manipulating GO and microarrays
- GPfit-1.0-8 Gaussian Processes Modeling
- GSA-1.03.1 Gene Set Analysis
- GSEABase-1.56.0 Gene set enrichment data structures and methods
- GSVA-1.42.0 Gene Set Variation Analysis for microarray and RNA-seq data
- GUTS-1.1.1 Fast Calculation of the Likelihood of a Stochastic Survival Model
- GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
- GWASTools-1.40.0 Tools for Genome Wide Association Studies
- GenSA-1.1.7 Generalized Simulated Annealing
- GeneNet-1.2.15 Modeling and Inferring Gene Networks
- GenomeGraphs 1.46.0
- GenomeInfoDb-1.30.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
- GenomeInfoDbData-1.2.7 Species and taxonomy ID look up tables used by GenomeInfoDb
- GenomicAlignments-1.30.0 Representation and manipulation of short genomic alignments
- GenomicFeatures-1.46.1 Conveniently import and query gene models
- GenomicFiles-1.30.0 Distributed computing by file or by range
- GenomicRanges-1.46.1 Representation and manipulation of genomic intervals
- GetoptLong-1.0.5 Parsing Command-Line Arguments and Simple Variable Interpolation
- GillespieSSA-0.6.1 Gillespie’s Stochastic Simulation Algorithm (SSA)
- Glimma-2.4.0 Interactive HTML graphics
- GlobalOptions-0.1.2 Generate Functions to Get or Set Global Options
- Gmisc-2.1.0 Descriptive Statistics, Transition Plots, and More
- GreyListChIP-1.26.0 Grey Lists – Mask Artefact Regions Based on ChIP Inputs
- Gviz-1.38.0 Plotting data and annotation information along genomic coordinates
- GxEScanR-2.0.2 Run GWAS/GWEIS Scans Using Binary Dosage Files
- HDF5Array-1.22.1 HDF5 backend for DelayedArray objects
- HMMcopy-1.36.0 Copy number prediction with correction for GC and mappability bias for HTS data
- HSMMSingleCell-1.14.0 Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
- HWxtest-1.1.9 Exact Tests for Hardy-Weinberg Proportions
- HaploSim-1.8.4 Functions to simulate haplotypes
- HiddenMarkov-1.8-13 Hidden Markov Models
- Hmisc-4.6-0 Harrell Miscellaneous
- Homo.sapiens-1.3.1 Annotation package for the Homo.sapiens object
- IDPmisc-1.1.20 ‘Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)’
- IHW-1.22.0 Independent Hypothesis Weighting
- IRanges-2.28.0 Foundation of integer range manipulation in Bioconductor
- IRdisplay-1.0 ‘Jupyter’ Display Machinery
- ISOcodes-2021.02.24 Selected ISO Codes
- IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
- InteractionSet-1.22.0 Base Classes for Storing Genomic Interaction Data
- Iso-0.0-18.1 Functions to Perform Isotonic Regression
- JADE-2.0-3 Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria
- JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J. Buttlar
- KEGGREST-1.34.0 Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
- KEGGgraph-1.54.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
- KODAMA-1.8 Knowledge Discovery by Accuracy Maximization
- KernSmooth-2.23-20 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
- LaplacesDemon-16.1.6 Complete Environment for Bayesian Inference
- LearnBayes-2.15.1 Functions for Learning Bayesian Inference
- Lmoments-1.3-1 L-Moments and Quantile Mixtures
- LogicReg-1.6.4 Logic Regression
- LymphoSeq-1.22.0 Analyze high-throughput sequencing of T and B cell receptors
- LymphoSeqDB-0.99.2 LymphoSeq annotation databases
- MAGeCKFlute-1.14.0 Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
- MALDIquant-1.20 Quantitative Analysis of Mass Spectrometry Data
- MASS-7.3-54 Support Functions and Datasets for Venables and Ripley’s MASS
- MAST-1.20.0 Model-based Analysis of Single Cell Transcriptomics
- MCMCglmm-2.32 MCMC Generalised Linear Mixed Models
- MCMCpack-1.6-0 Markov Chain Monte Carlo (MCMC) Package
- MIIVsem-0.5.8 Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
- MPV-1.57 Data Sets from Montgomery, Peck and Vining
- MatchIt-4.3.0 Nonparametric Preprocessing for Parametric Causal Inference
- Matching-4.9-11 Multivariate and Propensity Score Matching with Balance Optimization
- Matrix-1.3-4 Sparse and Dense Matrix Classes and Methods
- MatrixEQTL-2.3 Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
- MatrixGenerics-1.6.0 S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
- MatrixModels-0.5-0 Modelling with Sparse and Dense Matrices
- Mfuzz-2.54.0 Soft clustering of time series gene expression data
- ModelMetrics-1.2.2.2 Rapid Calculation of Model Metrics
- NADA-1.6-1.1 Nondetects and Data Analysis for Environmental Data
- NCmisc-1.1.6 Miscellaneous Functions for Creating Adaptive Functions and Scripts
- NISTunits-1.0.1 Fundamental Physical Constants and Unit Conversions from NIST
- NLP-0.2-1 Natural Language Processing Infrastructure
- NOISeq-2.38.0 Exploratory analysis and differential expression for RNA-seq data
- OceanView-1.0.6 Visualisation of Oceanographic Data and Model Output
- OrganismDbi-1.36.0 Software to enable the smooth interfacing of different database packages
- PBSddesolve-1.12.6 Solver for Delay Differential Equations
- PCAmatchR-0.3.0 Match Cases to Controls Based on Genotype Principal Components
- PFAM.db-3.14.0 A set of protein ID mappings for PFAM
- PICS-2.38.0 Probabilistic inference of ChIP-seq
- ParamHelpers-1.14 Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
- PermAlgo-1.1 Permutational Algorithm to Simulate Survival Data
- PoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log linear model
- PolynomF-2.0-3 Polynomials in R
- PresenceAbsence-1.1.9 Presence-Absence Model Evaluation.
- ProtGenerics-1.26.0 Generic infrastructure for Bioconductor mass spectrometry packages
- QUIC-1.1.1 Regularized Sparse Inverse Covariance Matrix Estimation
- R.cache-0.15.0 Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations
- R.matlab-3.6.2 Read and Write MAT Files and Call MATLAB from Within R
- R.methodsS3-1.8.1 S3 Methods Simplified
- R.oo-1.24.0 R Object-Oriented Programming with or without References
- R.rsp-0.44.0 Dynamic Generation of Scientific Reports
- R.utils-2.11.0 Various Programming Utilities
- R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
- R2jags-0.7-1 Using R to Run ‘JAGS’
- R6-2.5.1 Encapsulated Classes with Reference Semantics
- RANN-2.6.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
- RBGL-1.70.0 An interface to the BOOST graph library
- RCAL-2.0 Regularized Calibrated Estimation
- RCircos-1.2.1 Circos 2D Track Plot
- RColorBrewer-1.1-2 ColorBrewer Palettes
- RCurl-1.98-1.5 General Network (HTTP/FTP/…) Client Interface for R
- REDCapR-1.0.0 Interaction Between R and REDCap
- RGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation Analysis for Multiblock Data
- RInside-0.2.16 C++ Classes to Embed R in C++ (and C) Applications
- RItools-0.1-17 Randomization Inference Tools
- RJSONIO-1.3-1.6 Serialize R Objects to JSON, JavaScript Object Notation
- RLRsim-3.1-6 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models
- RMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix Theory
- RNASeqPower-1.34.0 Sample size for RNAseq studies
- RNeXML-2.4.5 Semantically Rich I/O for the ‘NeXML’ Format
- RNifti-1.3.1 Fast R and C++ Access to NIfTI Images
- ROCR-1.0-11 Visualizing the Performance of Scoring Classifiers
- ROI-1.0-0 R Optimization Infrastructure
- ROI.plugin.glpk-1.0-0 ‘ROI’ Plug-in ‘GLPK’
- RPMM-1.25 Recursively Partitioned Mixture Model
- RPostgreSQL-0.7-3 R Interface to the ‘PostgreSQL’ Database System
- RPresto-1.3.7 DBI Connector to Presto
- RProtoBuf-0.4.17 R Interface to the ‘Protocol Buffers’ ‘API’ (Version 2 or 3)
- RProtoBufLib-2.6.0 C++ headers and static libraries of Protocol buffers
- RSNNS-0.4-14 Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
- RSQLite-2.2.8 ‘SQLite’ Interface for R
- RSclient-0.7-6 Client for Rserve
- RSpectra-0.16-0 Solvers for Large-Scale Eigenvalue and SVD Problems
- RUnit-0.4.32 R Unit Test Framework
- RWeka-0.4-43 R/Weka Interface
- RWekajars-3.9.3-2 R/Weka Interface Jars
- Rborist-0.2-3 Extensible, Parallelizable Implementation of the Random Forest Algorithm
- Rcgmin-2013-2.21 Conjugate Gradient Minimization of Nonlinear Functions
- Rcpp-1.0.7 Seamless R and C++ Integration
- RcppAnnoy-0.0.19 ‘Rcpp’ Bindings for ‘Annoy’, a Library for Approximate Nearest Neighbors
- RcppArmadillo-0.10.7.0.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library
- RcppCCTZ-0.2.9 ‘Rcpp’ Bindings for the ‘CCTZ’ Library
- RcppDate-0.0.3 ‘date’ C++ Header Library for Date and Time Functionality
- RcppEigen-0.3.3.9.1 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra Library
- RcppGSL-0.3.10 ‘Rcpp’ Integration for ‘GNU GSL’ Vectors and Matrices
- RcppHNSW-0.3.0 ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest Neighbors
- RcppNumerical-0.4-0 ‘Rcpp’ Integration for Numerical Computing Libraries
- RcppParallel-5.1.4 Parallel Programming Tools for ‘Rcpp’
- RcppProgress-0.4.2 An Interruptible Progress Bar with OpenMP Support for C++ in R Packages
- RcppRoll-0.3.0 Efficient Rolling / Windowed Operations
- RcppZiggurat-0.1.6 ‘Rcpp’ Integration of Different “Ziggurat” Normal RNG Implementations
- Rdpack-2.1.2 Update and Manipulate Rd Documentation Objects
- Rdsdp-1.0.5.1 R Interface to DSDP Semidefinite Programming Library
- RefFreeEWAS-2.2 EWAS using Reference-Free DNA Methylation Mixture Deconvolution
- ReportingTools-2.34.0 Tools for making reports in various formats
- Rfast-2.0.3 A Collection of Efficient and Extremely Fast R Functions
- Rglpk-0.6-4 R/GNU Linear Programming Kit Interface
- Rgraphviz-2.38.0 Provides plotting capabilities for R graph objects
- Rhdf5lib-1.16.0 hdf5 library as an R package
- Rhpc-0.21-247 Permits apply() Style Dispatch for ‘HPC’
- Rhtslib-1.26.0 HTSlib high-throughput sequencing library as an R package
- Ringo-1.58.0 R Investigation of ChIP-chip Oligoarrays
- Rlabkey-2.8.1 Data Exchange Between R and ‘LabKey’ Server
- Rmpi-0.6-9.2 Interface (Wrapper) to MPI (Message-Passing Interface)
- Rook-1.1-1 Rook - a web server interface for R
- Rsamtools-2.10.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
- Rserve-1.7-3.1 Binary R server
- Rsolnp-1.16 General Non-Linear Optimization
- Rssa-1.0.4 A Collection of Methods for Singular Spectrum Analysis
- Rsubread-2.8.1 Mapping, quantification and variant analysis of sequencing data
- Rtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
- Rttf2pt1-1.3.9 ‘ttf2pt1’ Program
- Rvmmin-2018-4.17.1 Variable Metric Nonlinear Function Minimization
- S4Vectors-0.32.3 Foundation of vector-like and list-like containers in Bioconductor
- SBdecomp-1.1 Estimation of the Proportion of SB Explained by Confounders
- SDMTools-1.1-221.2 Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
- SKAT-2.0.1 SNP-Set (Sequence) Kernel Association Test
- SNPRelate-1.28.0 Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)
- SNPassoc-2.0-2 SNPs-Based Whole Genome Association Studies
- SOAR-0.99-11 Memory management in R by delayed assignments
- SPAtest-3.1.2 Score Test and Meta-Analysis Based on Saddlepoint Approximation
- SPIA-2.46.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
- SQUAREM-2021.1 Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
- ScaledMatrix-1.2.0 Creating a DelayedMatrix of Scaled and Centered Values
- SemiPar-1.0-4.2 Semiparametic Regression
- SeqArray-1.34.0 Data management of large-scale whole-genome sequence variant calls
- SeqVarTools-1.32.0 Tools for variant data
- ShortRead-1.52.0 FASTQ input and manipulation
- SignifReg-4.2 Consistent Significance Controlled Variable Selection in Generalized Linear Regression
- SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
- SingleCellExperiment-1.16.0 S4 Classes for Single Cell Data
- SnowballC-0.7.0 Snowball Stemmers Based on the C ‘libstemmer’ UTF-8 Library
- SparseM-1.81 Sparse Linear Algebra
- StanHeaders-2.21.0-7 C++ Header Files for Stan
- SummarizedExperiment-1.24.0 SummarizedExperiment container
- SuperLearner-2.0-28 Super Learner Prediction
- SuppDists-1.1-9.5 Supplementary Distributions
- TFBSTools-1.32.0 Software Package for Transcription Factor Binding Site (TFBS) Analysis
- TFMPvalue-0.0.8 Efficient and Accurate P-Value Computation for Position Weight Matrices
- TFisher-0.2.0 Optimal Thresholding Fisher’s P-Value Combination Method
- TH.data-1.1-0 TH’s Data Archive
- TMB-1.7.22 Template Model Builder: A General Random Effect Tool Inspired by ‘ADMB’
- TTR-0.24.2 Technical Trading Rules
- TeachingDemos-2.12 Demonstrations for Teaching and Learning
- TitanCNA-1.32.0 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
- TraMineR-2.2-2 Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
- TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)
- UpSetR-1.4.0 A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
- V8-3.4.2 Embedded JavaScript and WebAssembly Engine for R
- VGAM-1.1-5 Vector Generalized Linear and Additive Models
- VIM-6.1.1 Visualization and Imputation of Missing Values
- VSURF-1.1.0 Variable Selection Using Random Forests
- VariantAnnotation-1.40.0 Annotation of Genetic Variants
- VennDiagram-1.7.0 Generate High-Resolution Venn and Euler Plots
- WeightSVM-1.7-9 Subject Weighted Support Vector Machines
- WikidataQueryServiceR-1.0.0 API Client Library for ‘Wikidata Query Service’
- WikidataR-2.3.1 Read-Write API Client Library for Wikidata
- WikipediR-1.5.0 A MediaWiki API Wrapper
- Wrench-1.12.0 Wrench normalization for sparse count data
- WriteXLS-6.3.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files
- XML-3.99-0.8 Tools for Parsing and Generating XML Within R and S-Plus
- XVector-0.34.0 Foundation of external vector representation and manipulation in Bioconductor
- abc-2.1 Tools for Approximate Bayesian Computation (ABC)
- abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)
- abe-3.0.1 Augmented Backward Elimination
- abind-1.4-5 Combine Multidimensional Arrays
- acepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformations
- adabag-4.2 Applies Multiclass AdaBoost.M1, SAMME and Bagging
- ade4-1.7-18 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
- admisc-0.20 Adrian Dusa’s Miscellaneous
- affxparser-1.66.0 Affymetrix File Parsing SDK
- affy-1.72.0 Methods for Affymetrix Oligonucleotide Arrays
- affycoretools-1.66.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
- affyio-1.64.0 Tools for parsing Affymetrix data files
- aggregation-1.0.1 p-Value Aggregation Methods
- akima-0.6-2.2 Interpolation of Irregularly and Regularly Spaced Data
- alabama-2015.3-1 Constrained Nonlinear Optimization
- alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
- amap-0.8-18 Another Multidimensional Analysis Package
- animation-2.7 A Gallery of Animations in Statistics and Utilities to Create Animations
- annaffy-1.66.0 Annotation tools for Affymetrix biological metadata
- annotate-1.72.0 Annotation for microarrays
- aod-1.3.1 Analysis of Overdispersed Data
- ape-5.5 Analyses of Phylogenetics and Evolution
- apeglm-1.16.0 Approximate posterior estimation for GLM coefficients
- aplot-0.1.1 Decorate a ‘ggplot’ with Associated Information
- argparse-2.1.2 Command Line Optional and Positional Argument Parser
- argparser-0.7.1 Command-Line Argument Parser
- arm-1.12-2 Data Analysis Using Regression and Multilevel/Hierarchical Models
- arsenal-3.6.3 An Arsenal of ‘R’ Functions for Large-Scale Statistical Summaries
- arules-1.7-1 Mining Association Rules and Frequent Itemsets
- ash-1.0-15 David Scott’s ASH Routines
- ashr-2.2-47 Methods for Adaptive Shrinkage, using Empirical Bayes
- askpass-1.1 Safe Password Entry for R, Git, and SSH
- asnipe-1.1.16 Animal Social Network Inference and Permutations for Ecologists
- assertive-0.3-6 Readable Check Functions to Ensure Code Integrity
- assertive.base-0.0-9 A Lightweight Core of the ‘assertive’ Package
- assertive.code-0.0-3 Assertions to Check Properties of Code
- assertive.data-0.0-3 Assertions to Check Properties of Data
- assertive.data.uk-0.0-2 Assertions to Check Properties of Strings
- assertive.data.us-0.0-2 Assertions to Check Properties of Strings
- assertive.datetimes-0.0-3 Assertions to Check Properties of Dates and Times
- assertive.files-0.0-2 Assertions to Check Properties of Files
- assertive.matrices-0.0-2 Assertions to Check Properties of Matrices
- assertive.models-0.0-2 Assertions to Check Properties of Models
- assertive.numbers-0.0-2 Assertions to Check Properties of Numbers
- assertive.properties-0.0-4 Assertions to Check Properties of Variables
- assertive.reflection-0.0-5 Assertions for Checking the State of R
- assertive.sets-0.0-3 Assertions to Check Properties of Sets
- assertive.strings-0.0-3 Assertions to Check Properties of Strings
- assertive.types-0.0-3 Assertions to Check Types of Variables
- assertthat-0.2.1 Easy Pre and Post Assertions
- audio-0.1-8 Audio Interface for R
- aws-2.5-1 Adaptive Weights Smoothing
- aws.ec2metadata-0.2.0 Get EC2 Instance Metadata
- aws.s3-0.3.21 ‘AWS S3’ Client Package
- aws.signature-0.6.0 Amazon Web Services Request Signatures
- awsMethods-1.1-1 Class and Methods Definitions for Packages ‘aws’, ‘adimpro’, ‘fmri’, ‘dwi’
- babelgene-21.4 Gene Orthologs for Model Organisms in a Tidy Data Format
- backports-1.3.0 Reimplementations of Functions Introduced Since R-3.0.0
- bacr-1.0.1 Bayesian Adjustment for Confounding
- bamsignals-1.26.0 Extract read count signals from bam files
- bartMachine-1.2.6 Bayesian Additive Regression Trees
- bartMachineJARs-1.1 bartMachine JARs
- base built in
- base64-2.0 Base64 Encoder and Decoder
- base64enc-0.1-3 Tools for base64 encoding
- base64url-1.4 Fast and URL-Safe Base64 Encoder and Decoder
- batchmeans-1.0-4 Consistent Batch Means Estimation of Monte Carlo Standard Errors
- batchtools-0.9.15 Tools for Computation on Batch Systems
- baySeq-2.28.0 Empirical Bayesian analysis of patterns of differential expression in count data
- bayesm-3.1-4 Bayesian Inference for Marketing/Micro-Econometrics
- bayesplot-1.8.1 Plotting for Bayesian Models
- bbmle-1.0.24 Tools for General Maximum Likelihood Estimation
- bdsmatrix-1.3-4 Routines for Block Diagonal Symmetric Matrices
- beachmat-2.10.0 Compiling Bioconductor to Handle Each Matrix Type
- beanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot)
- beeswarm-0.4.0 The Bee Swarm Plot, an Alternative to Stripchart
- benchmark-0.3-6 Benchmark Experiments Toolbox
- betareg-3.1-4 Beta Regression
- bezier-1.1.2 Toolkit for Bezier Curves and Splines
- bibtex-0.4.2.3 Bibtex Parser
- biglm-0.9-2.1 Bounded Memory Linear and Generalized Linear Models
- bigmemory-4.5.36 Manage Massive Matrices with Shared Memory and Memory-Mapped Files
- bigmemory.sri-0.1.3 A shared resource interface for Bigmemory Project packages
- bindr-0.1.1 Parametrized Active Bindings
- bindrcpp-0.2.2 An ‘Rcpp’ Interface to Active Bindings
- bio3d-2.4-2 Biological Structure Analysis
- biom-0.3.12 An interface package (beta) for the BIOM file format.
- biomaRt-2.50.1 Interface to BioMart databases (i.e. Ensembl)
- biomformat-1.22.0 An interface package for the BIOM file format
- biomod2-3.5.1 Ensemble Platform for Species Distribution Modeling
- biovizBase-1.42.0 Basic graphic utilities for visualization of genomic data.
- bit-4.0.4 Classes and Methods for Fast Memory-Efficient Boolean Selections
- bit64-4.0.5 A S3 Class for Vectors of 64bit Integers
- bitops-1.0-7 Bitwise Operations
- blavaan-0.3-17 Bayesian Latent Variable Analysis
- blob-1.2.2 A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’)
- bmp-0.3 Read Windows Bitmap (BMP) Images
- bnlearn-4.7 Bayesian Network Structure Learning, Parameter Learning and Inference
- bold-1.2.0 Interface to Bold Systems API
- bookdown-0.24 Authoring Books and Technical Documents with R Markdown
- boot-1.3-28 Bootstrap Functions (Originally by Angelo Canty for S)
- bootstrap-2019.6 Functions for the Book “An Introduction to the Bootstrap”
- breakaway-3.0 Species Richness Estimation and Modeling
- brew-1.0-6 Templating Framework for Report Generation
- brglm-0.7.2 Bias Reduction in Binomial-Response Generalized Linear Models
- bridgedist-0.1.0 An Implementation of the Bridge Distribution with Logit-Link as in Wang and Louis (2003)
- bridgesampling-1.1-2 Bridge Sampling for Marginal Likelihoods and Bayes Factors
- brio-1.1.2 Basic R Input Output
- brms-2.16.1 Bayesian Regression Models using ‘Stan’
- broom-0.7.10 Convert Statistical Objects into Tidy Tibbles
- broom.helpers-1.4.0 Helpers for Model Coefficients Tibbles
- broom.mixed-0.2.7 Tidying Methods for Mixed Models
- bslib-0.3.1 Custom ‘Bootstrap’ ‘Sass’ Themes for ‘shiny’ and ‘rmarkdown’
- bst-0.3-23 Gradient Boosting
- bumphunter-1.36.0 Bump Hunter
- cNORM-2.1.0 Continuous Norming
- cSEM-0.4.0 Composite-Based Structural Equation Modeling
- caTools-1.18.2 Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
- cachem-1.0.6 Cache R Objects with Automatic Pruning
- calibrate-1.7.7 Calibration of Scatterplot and Biplot Axes
- callr-3.7.0 Call R from R
- car-3.0-11 Companion to Applied Regression
- carData-3.0-4 Companion to Applied Regression Data Sets
- caret-6.0-90 Classification and Regression Training
- catdata-1.2.2 Categorical Data
- celestial-1.4.6 Collection of Common Astronomical Conversion Routines and Functions
- cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
- cgdsr-1.3.0 R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)
- cghFLasso-0.2-1 Detecting hot spot on CGH array data with fused lasso regression.
- checkmate-2.0.0 Fast and Versatile Argument Checks
- chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
- chipseq-1.44.0 chipseq: A package for analyzing chipseq data
- chromVAR-1.16.0 Chromatin Variation Across Regions
- chron-2.3-56 Chronological Objects which can Handle Dates and Times
- circlize-0.4.13 Circular Visualization
- circular-0.4-93 Circular Statistics
- clValid-0.7 Validation of Clustering Results
- class-7.3-19 Functions for Classification
- classInt-0.4-3 Choose Univariate Class Intervals
- cli-3.1.0 Helpers for Developing Command Line Interfaces
- clipr-0.7.1 Read and Write from the System Clipboard
- clisymbols-1.2.0 Unicode Symbols at the R Prompt
- clue-0.3-60 Cluster Ensembles
- cluster-2.1.2 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al.
- clusterGeneration-1.3.7 Random Cluster Generation (with Specified Degree of Separation)
- clusterProfiler-4.2.0 A universal enrichment tool for interpreting omics data
- clusterRepro-0.9 Reproducibility of Gene Expression Clusters
- clustree-0.4.3 Visualise Clusterings at Different Resolutions
- cobalt-4.3.1 Covariate Balance Tables and Plots
- cobs-1.3-4 Constrained B-Splines (Sparse Matrix Based)
- coda-0.19-4 Output Analysis and Diagnostics for MCMC
- codetools-0.2-18 Code Analysis Tools for R
- coin-1.4-2 Conditional Inference Procedures in a Permutation Test Framework
- colorRamps-2.3 Builds color tables
- colorspace-2.0-2 A Toolbox for Manipulating and Assessing Colors and Palettes
- colourpicker-1.1.1 A Colour Picker Tool for Shiny and for Selecting Colours in Plots
- combinat-0.0-8 combinatorics utilities
- commonmark-1.7 High Performance CommonMark and Github Markdown Rendering in R
- compare-0.2-6 Comparing Objects for Differences
- compiler built in
- compositions-2.0-2 Compositional Data Analysis
- conditionz-0.1.0 Control How Many Times Conditions are Thrown
- config-0.3.1 Manage Environment Specific Configuration Values
- conflicted-1.0.4 An Alternative Conflict Resolution Strategy
- conquer-1.2.0 Convolution-Type Smoothed Quantile Regression
- copCAR-2.0-4 Fitting the copCAR Regression Model for Discrete Areal Data
- copula-1.0-1 Multivariate Dependence with Copulas
- copynumber-1.34.0 Segmentation of single- and multi-track copy number data by penalized least squares regression.
- corpcor-1.6.10 Efficient Estimation of Covariance and (Partial) Correlation
- corrplot-0.90 Visualization of a Correlation Matrix
- covr-3.5.1 Test Coverage for Packages
- cowplot-1.1.1 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
- coxed-0.3.3 Duration-Based Quantities of Interest for the Cox Proportional Hazards Model
- coxme-2.2-16 Mixed Effects Cox Models
- cpp11-0.4.0 A C++11 Interface for R’s C Interface
- crayon-1.4.2 Colored Terminal Output
- credentials-1.3.1 Tools for Managing SSH and Git Credentials
- crosstalk-1.1.1 Inter-Widget Interactivity for HTML Widgets
- crul-1.1.0 HTTP Client
- csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
- ctmle-0.1.2 Collaborative Targeted Maximum Likelihood Estimation
- cubature-2.0.4.2 Adaptive Multivariate Integration over Hypercubes
- cubelyr-1.0.1 A Data Cube ‘dplyr’ Backend
- cummeRbund-2.36.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
- curl-4.3.2 A Modern and Flexible Web Client for R
- curry-0.1.1 Partial Function Application with %<%, %-<%, and %><%
- cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
- cyclocomp-1.1.0 Cyclomatic Complexity of R Code
- cytolib-2.6.0 C++ infrastructure for representing and interacting with the gated cytometry data
- d3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R
- dHSIC-2.1 Independence Testing via Hilbert Schmidt Independence Criterion
- dada2-1.22.0 Accurate, high-resolution sample inference from amplicon sequencing data
- data.table-1.14.2 Extension of
data.frame
- data.tree-1.0.0 General Purpose Hierarchical Data Structure
- datasets built in
- dbarts-0.9-20 Discrete Bayesian Additive Regression Trees Sampler
- dbplyr-2.1.1 A ‘dplyr’ Back End for Databases
- dbscan-1.1-8 Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms
- ddalpha-1.3.11 Depth-Based Classification and Calculation of Data Depth
- deSolve-1.30 Solvers for Initial Value Problems of Differential Equations (‘ODE’, ‘DAE’, ‘DDE’)
- deal-1.2-39 Learning Bayesian Networks with Mixed Variables
- debugme-1.1.0 Debug R Packages
- degreenet-1.3-3 Models for Skewed Count Distributions Relevant to Networks
- deldir-1.0-6 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
- dendextend-1.15.2 Extending ‘dendrogram’ Functionality in R
- derfinder-1.28.0 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
- derfinderHelper-1.28.0 derfinder helper package
- desc-1.4.0 Manipulate DESCRIPTION Files
- descr-1.1.5 Descriptive Statistics
- devtools-2.4.2 Tools to Make Developing R Packages Easier
- dfidx-0.0-4 Indexed Data Frames
- dfoptim-2020.10-1 Derivative-Free Optimization
- diagram-1.6.5 Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams
- dials-0.0.10 Tools for Creating Tuning Parameter Values
- diamonds-1.0-5 Analysis and sampling grids from diamond partitions
- dichromat-2.0-0 Color Schemes for Dichromats
- diffobj-0.3.5 Diffs for R Objects
- diffusionMap-1.2.0 Diffusion Map
- digest-0.6.28 Create Compact Hash Digests of R Objects
- dimRed-0.2.3 A Framework for Dimensionality Reduction
- diptest-0.76-0 Hartigan’s Dip Test Statistic for Unimodality - Corrected
- dismo-1.3-5 Species Distribution Modeling
- distillery-1.2-1 Method Functions for Confidence Intervals and to Distill Information from an Object
- distr-2.8.0 Object Oriented Implementation of Distributions
- distrEx-2.8.0 Extensions of Package ‘distr’
- distributional-0.2.2 Vectorised Probability Distributions
- diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis Package
- doBy-4.6.11 Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
- doMC-1.3.7 Foreach Parallel Adaptor for ‘parallel’
- doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
- doParallel-1.0.16 Foreach Parallel Adaptor for the ‘parallel’ Package
- doRNG-1.8.2 Generic Reproducible Parallel Backend for ‘foreach’ Loops
- doSNOW-1.0.19 Foreach Parallel Adaptor for the ‘snow’ Package
- dotCall64-1.0-1 Enhanced Foreign Function Interface Supporting Long Vectors
- downloader-0.4 Download Files over HTTP and HTTPS
- dplyr-1.0.7 A Grammar of Data Manipulation
- dqrng-0.3.0 Fast Pseudo Random Number Generators
- dr-3.0.10 Methods for Dimension Reduction for Regression
- drc-3.0-1 Analysis of Dose-Response Curves
- drgee-1.1.10 Doubly Robust Generalized Estimating Equations
- drugCombo-1.2.1 Drug Interaction Modeling Based on Loewe Additivity Following Harbron’s Approach
- dtangle-2.0.9 Cell Type Deconvolution from Gene Expressions
- dtplyr-1.1.0 Data Table Back-End for ‘dplyr’
- dtw-1.22-3 Dynamic Time Warping Algorithms
- dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
- dygraphs-1.1.1.6 Interface to ‘Dygraphs’ Interactive Time Series Charting Library
- dynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering Dendrograms
- e1071-1.7-9 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
- earth-5.3.1 Multivariate Adaptive Regression Splines
- edgeR-3.36.0 Empirical Analysis of Digital Gene Expression Data in R
- elasticnet-1.3 Elastic-Net for Sparse Estimation and Sparse PCA
- elementR-1.3.7 An Framework for Reducing Elemental LAICPMS Data from Solid Structures
- ellipse-0.4.2 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
- ellipsis-0.3.2 Tools for Working with …
- emdbook-1.3.12 Support Functions and Data for “Ecological Models and Data”
- emulator-1.2-21 Bayesian Emulation of Computer Programs
- energy-1.7-8 E-Statistics: Multivariate Inference via the Energy of Data
- enrichplot-1.14.1 Visualization of Functional Enrichment Result
- ensembldb-2.18.2 Utilities to create and use Ensembl-based annotation databases
- entropy-1.3.1 Estimation of Entropy, Mutual Information and Related Quantities
- epitools-0.5-10.1 Epidemiology Tools
- ergm-4.1.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks
- ergm.count-4.0.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
- etrunct-0.1 Computes Moments of Univariate Truncated t Distribution
- europepmc-0.4.1 R Interface to the Europe PubMed Central RESTful Web Service
- evaluate-0.14 Parsing and Evaluation Tools that Provide More Details than the Default
- expm-0.999-6 Matrix Exponential, Log, ‘etc’
- expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
- extRemes-2.1-1 Extreme Value Analysis
- extrafont-0.17 Tools for using fonts
- extrafontdb-1.0 Package for holding the database for the extrafont package
- fANCOVA-0.6-1 Nonparametric Analysis of Covariance
- fail-1.3 File Abstraction Interface Layer (FAIL)
- fansi-0.5.0 ANSI Control Sequence Aware String Functions
- faraway-1.0.7 Functions and Datasets for Books by Julian Faraway
- farver-2.1.0 High Performance Colour Space Manipulation
- fastICA-1.2-3 FastICA Algorithms to Perform ICA and Projection Pursuit
- fastcluster-1.2.3 Fast Hierarchical Clustering Routines for R and ‘Python’
- fasterize-1.0.3 Fast Polygon to Raster Conversion
- fastmap-1.1.0 Fast Data Structures
- fastmatch-1.1-3 Fast ‘match()’ Function
- fastseg-1.40.0 fastseg - a fast segmentation algorithm
- fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
- fda-5.5.1 Functional Data Analysis
- fdrtool-1.2.16 Estimation of (Local) False Discovery Rates and Higher Criticism
- fds-1.8 Functional Data Sets
- feather-0.3.5 R Bindings to the Feather ‘API’
- ff-4.0.5 Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
- ffbase-0.13.3 Basic Statistical Functions for Package ‘ff’
- fftw-1.0-6 Fast FFT and DCT Based on the FFTW Library
- fftwtools-0.9-11 Wrapper for ‘FFTW3’ Includes: One-Dimensional, Two-Dimensional, Three-Dimensional, and Multivariate Transforms
- fgsea-1.20.0 Fast Gene Set Enrichment Analysis
- fields-13.3 Tools for Spatial Data
- filehash-2.4-2 Simple Key-Value Database
- filelock-1.0.2 Portable File Locking
- finalfit-1.0.3 Quickly Create Elegant Regression Results Tables and Plots when Modelling
- findpython-1.0.7 Functions to Find an Acceptable Python Binary
- fishMod-0.29 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta Log-Normal Models
- fit.models-0.64 Compare Fitted Models
- fitdistrplus-1.1-6 Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
- flashClust-1.01-2 Implementation of optimal hierarchical clustering
- flexclust-1.4-0 Flexible Cluster Algorithms
- flexmix-2.3-17 Flexible Mixture Modeling
- flowClust-3.32.0 Clustering for Flow Cytometry
- flowCore-2.6.0 flowCore: Basic structures for flow cytometry data
- flowStats-4.6.0 Statistical methods for the analysis of flow cytometry data
- flowViz-1.58.0 Visualization for flow cytometry
- flowWorkspace-4.6.0 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
- fma-2.4 Data Sets from “Forecasting: Methods and Applications” by Makridakis, Wheelwright & Hyndman (1998)
- fmri-1.9.6 Analysis of fMRI Experiments
- fontawesome-0.2.2 Easily Work with ‘Font Awesome’ Icons
- forcats-0.5.1 Tools for Working with Categorical Variables (Factors)
- foreach-1.5.1 Provides Foreach Looping Construct
- forecast-8.15 Forecasting Functions for Time Series and Linear Models
- foreign-0.8-81 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …
- forestplot-2.0.1 Advanced Forest Plot Using ‘grid’ Graphics
- forge-0.2.0 Casting Values into Shape
- formatR-1.11 Format R Code Automatically
- formula.tools-1.7.1 Programmatic Utilities for Manipulating Formulas, Expressions, Calls, Assignments and Other R Objects
- fossil-0.4.0 Palaeoecological and Palaeogeographical Analysis Tools
- fpc-2.2-9 Flexible Procedures for Clustering
- fpp-0.5 Data for “Forecasting: principles and practice”
- fracdiff-1.5-1 Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
- fs-1.5.0 Cross-Platform File System Operations Based on ‘libuv’
- fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
- furrr-0.2.3 Apply Mapping Functions in Parallel using Futures
- futile.logger-1.4.3 A Logging Utility for R
- futile.options-1.0.1 Futile Options Management
- future-1.23.0 Unified Parallel and Distributed Processing in R for Everyone
- future.apply-1.8.1 Apply Function to Elements in Parallel using Futures
- gWidgets2-1.0-8 Rewrite of gWidgets API for Simplified GUI Construction
- gWidgets2tcltk-1.0-6 Toolkit Implementation of gWidgets2 for tcltk
- gage-2.44.0 Generally Applicable Gene-set Enrichment for Pathway Analysis
- gam-1.20 Generalized Additive Models
- gamlss-5.3-4 Generalised Additive Models for Location Scale and Shape
- gamlss.data-6.0-1 Data for Generalised Additive Models for Location Scale and Shape
- gamlss.dist-5.3-2 Distributions for Generalized Additive Models for Location Scale and Shape
- gamlss.tr-5.1-7 Generating and Fitting Truncated `gamlss.family’ Distributions
- gamm4-0.2-6 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
- gap-1.2.3-1 Genetic Analysis Package
- gapfill-0.9.6-1 Fill Missing Values in Satellite Data
- gargle-1.2.0 Utilities for Working with Google APIs
- gaussquad-1.0-2 Collection of functions for Gaussian quadrature
- gbRd-0.4-11 Utilities for processing Rd objects and files
- gbm-2.1.8 Generalized Boosted Regression Models
- gclus-1.3.2 Clustering Graphics
- gcrma-2.66.0 Background Adjustment Using Sequence Information
- gdata-2.18.0 Various R Programming Tools for Data Manipulation
- gdistance-1.3-6 Distances and Routes on Geographical Grids
- gdsfmt-1.30.0 R Interface to CoreArray Genomic Data Structure (GDS) files
- gdtools-0.2.3 Utilities for Graphical Rendering
- gee-4.13-20 Generalized Estimation Equation Solver
- geepack-1.3-2 Generalized Estimating Equation Package
- geiger-2.0.7 Analysis of Evolutionary Diversification
- geneLenDataBase-1.30.0 Lengths of mRNA transcripts for a number of genomes
- genefilter-1.76.0 genefilter: methods for filtering genes from high-throughput experiments
- geneplotter-1.72.0 Graphics related functions for Bioconductor
- generics-0.1.1 Common S3 Generics not Provided by Base R Methods Related to Model Fitting
- geometry-0.4.5 Mesh Generation and Surface Tessellation
- gert-1.4.1 Simple Git Client for R
- getopt-1.20.3 C-Like ‘getopt’ Behavior
- ggExtra-0.9 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’ Enhancements
- ggbeeswarm-0.6.0 Categorical Scatter (Violin Point) Plots
- ggbio-1.42.0 Visualization tools for genomic data
- ggcyto-1.22.0 Visualize Cytometry data with ggplot
- ggdendro-0.1.22 Create Dendrograms and Tree Diagrams Using ‘ggplot2’
- ggfan-0.1.3 Summarise a Distribution Through Coloured Intervals
- ggforce-0.3.3 Accelerating ‘ggplot2’
- ggfun-0.0.4 Miscellaneous Functions for ‘ggplot2’
- ggnetwork-0.5.10 Geometries to Plot Networks with ‘ggplot2’
- ggnewscale-0.4.5 Multiple Fill and Colour Scales in ‘ggplot2’
- ggplot2-3.3.5 Create Elegant Data Visualisations Using the Grammar of Graphics
- ggplotify-0.1.0 Convert Plot to ‘grob’ or ‘ggplot’ Object
- ggpointdensity-0.1.0 A Cross Between a 2D Density Plot and a Scatter Plot
- ggpubr-0.4.0 ‘ggplot2’ Based Publication Ready Plots
- ggraph-2.0.5 An Implementation of Grammar of Graphics for Graphs and Networks
- ggrepel-0.9.1 Automatically Position Non-Overlapping Text Labels with ‘ggplot2’
- ggridges-0.5.3 Ridgeline Plots in ‘ggplot2’
- ggsci-2.9 Scientific Journal and Sci-Fi Themed Color Palettes for ‘ggplot2’
- ggsignif-0.6.3 Significance Brackets for ‘ggplot2’
- ggthemes-4.2.4 Extra Themes, Scales and Geoms for ‘ggplot2’
- ggtree-3.2.1 an R package for visualization of tree and annotation data
- ggvis-0.4.7 Interactive Grammar of Graphics
- gh-1.3.0 ‘GitHub’ ‘API’
- git2r-0.28.0 Provides Access to Git Repositories
- gitcreds-0.1.1 Query ‘git’ Credentials from ‘R’
- glasso-1.11 Graphical Lasso: Estimation of Gaussian Graphical Models
- gld-2.6.2 Estimation and Use of the Generalised (Tukey) Lambda Distribution
- gllvm-1.3.1 Generalized Linear Latent Variable Models
- glmmML-1.1.1 Generalized Linear Models with Clustering
- glmmTMB-1.1.2.3 Generalized Linear Mixed Models using Template Model Builder
- glmnet-4.1-2 Lasso and Elastic-Net Regularized Generalized Linear Models
- glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model
- globals-0.14.0 Identify Global Objects in R Expressions
- glue-1.4.2 Interpreted String Literals
- gmm-1.6-6 Generalized Method of Moments and Generalized Empirical Likelihood
- gmodels-2.18.1 Various R Programming Tools for Model Fitting
- gmp-0.6-2 Multiple Precision Arithmetic
- gnumeric-0.7-8 Read Data from Files Readable by ‘gnumeric’
- goftest-1.2-3 Classical Goodness-of-Fit Tests for Univariate Distributions
- gomms-1.0 GLM-Based Ordination Method
- googledrive-2.0.0 An Interface to Google Drive
- googlesheets4-1.0.0 Access Google Sheets using the Sheets API V4
- goseq-1.46.0 Gene Ontology analyser for RNA-seq and other length biased data
- gower-0.2.2 Gower’s Distance
- gplots-3.1.1 Various R Programming Tools for Plotting Data
- grDevices built in
- grImport2-0.2-0 Importing ‘SVG’ Graphics
- graph-1.72.0 graph: A package to handle graph data structures
- graphics built in
- graphlayouts-0.7.1 Additional Layout Algorithms for Network Visualizations
- grf-2.0.2 Generalized Random Forests
- grid built in
- gridBase-0.4-7 Integration of base and grid graphics
- gridExtra-2.3 Miscellaneous Functions for “Grid” Graphics
- gridGraphics-0.5-1 Redraw Base Graphics Using ‘grid’ Graphics
- grpreg-3.4.0 Regularization Paths for Regression Models with Grouped Covariates
- gsalib-2.1 Utility Functions For GATK
- gsl-2.1-7 Wrapper for the Gnu Scientific Library
- gsubfn-0.7 Utilities for Strings and Function Arguments
- gsw-1.0-6 Gibbs Sea Water Functions
- gt-0.3.1 Easily Create Presentation-Ready Display Tables
- gtable-0.3.0 Arrange ‘Grobs’ in Tables
- gtools-3.9.2 Various R Programming Tools
- gtsummary-1.5.0 Presentation-Ready Data Summary and Analytic Result Tables
- h2o-3.34.0.3 R Interface for the ‘H2O’ Scalable Machine Learning Platform
- hal9001-0.4.1 The Scalable Highly Adaptive Lasso
- hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
- haplo.stats-1.8.7 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
- hardhat-0.1.6 Construct Modeling Packages
- haven-2.4.3 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
- hdf5r-1.3.4 Interface to the ‘HDF5’ Binary Data Format
- hdm-0.3.1 High-Dimensional Metrics
- hdrcde-3.4 Highest Density Regions and Conditional Density Estimation
- heatmap3-1.1.9 An Improved Heatmap Package
- here-1.0.1 A Simpler Way to Find Your Files
- hexbin-1.28.2 Hexagonal Binning Routines
- hgu133plus2.db-3.13.0 Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)
- highr-0.9 Syntax Highlighting for R Source Code
- hms-1.1.1 Pretty Time of Day
- hopach-2.54.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
- htmlTable-2.3.0 Advanced Tables for Markdown/HTML
- htmltools-0.5.2 Tools for HTML
- htmlwidgets-1.5.4 HTML Widgets for R
- httpcode-0.3.0 ‘HTTP’ Status Code Helper
- httpuv-1.6.3 HTTP and WebSocket Server Library
- httr-1.4.2 Tools for Working with URLs and HTTP
- huge-1.3.5 High-Dimensional Undirected Graph Estimation
- hunspell-3.0.1 High-Performance Stemmer, Tokenizer, and Spell Checker
- hwriter-1.3.2 HTML Writer - Outputs R objects in HTML format
- hypergate-0.8.3 Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry
- ica-1.0-2 Independent Component Analysis
- idr-1.2 Irreproducible discovery rate
- ids-1.0.1 Generate Random Identifiers
- ie2misc-0.8.6 Irucka Embry’s Miscellaneous USGS Functions
- igraph-1.2.7 Network Analysis and Visualization
- igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
- illuminaio-0.36.0 Parsing Illumina Microarray Output Files
- image.binarization-0.1.2 Binarize Images for Enhancing Optical Character Recognition
- imager-0.42.10 Image Processing Library Based on ‘CImg’
- imagerExtra-1.3.2 Extra Image Processing Library Based on ‘imager’
- impute-1.68.0 impute: Imputation for microarray data
- ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
- infer-1.0.0 Tidy Statistical Inference
- inferference-1.0.2 Methods for Causal Inference with Interference
- influenceR-0.1.0.1 Software Tools to Quantify Structural Importance of Nodes in a Network
- infotheo-1.2.0 Information-Theoretic Measures
- ini-0.3.1 Read and Write ‘.ini’ Files
- inline-0.3.19 Functions to Inline C, C++, Fortran Function Calls from R
- interactiveDisplayBase-1.32.0 Base package for enabling powerful shiny web displays of Bioconductor objects
- intergraph-2.0-2 Coercion Routines for Network Data Objects
- interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
- intrinsicDimension-1.2.0 Intrinsic Dimension Estimation
- inum-1.0-4 Interval and Enum-Type Representation of Vectors
- invgamma-1.1 The Inverse Gamma Distribution
- iotools-0.3-2 I/O Tools for Streaming
- ipred-0.9-12 Improved Predictors
- irace-3.4.1 Iterated Racing for Automatic Algorithm Configuration
- irlba-2.3.3 Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices
- isoband-0.2.5 Generate Isolines and Isobands from Regularly Spaced Elevation Grids
- iterators-1.0.13 Provides Iterator Construct
- itertools-0.1-3 Iterator Tools
- its-1.1.8 Irregular Time Series
- janeaustenr-0.1.5 Jane Austen’s Complete Novels
- jiebaR-0.11 Chinese Text Segmentation
- jiebaRD-0.1 Chinese Text Segmentation Data for jiebaR Package
- jomo-2.7-2 Multilevel Joint Modelling Multiple Imputation
- jpeg-0.1-9 Read and write JPEG images
- jquerylib-0.1.4 Obtain ‘jQuery’ as an HTML Dependency Object
- jsonlite-1.7.2 A Simple and Robust JSON Parser and Generator for R
- jstable-1.0.7 Create Tables from Different Types of Regression
- karyoploteR-1.20.0 Plot customizable linear genomes displaying arbitrary data
- kedd-1.0.3 Kernel Estimator and Bandwidth Selection for Density and Its Derivatives
- kernlab-0.9-29 Kernel-Based Machine Learning Lab
- keyring-1.2.0 Access the System Credential Store from R
- kin.cohort-0.7 Analysis of Kin-Cohort Studies
- kinship2-1.8.5 Pedigree Functions
- klaR-0.6-15 Classification and Visualization
- knitr-1.36 A General-Purpose Package for Dynamic Report Generation in R
- knockoff-0.3.3 The Knockoff Filter for Controlled Variable Selection
- kohonen-3.0.10 Supervised and Unsupervised Self-Organising Maps
- ks-1.13.2 Kernel Smoothing
- kyotil-2021.5-14 Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
- labdsv-2.0-1 Ordination and Multivariate Analysis for Ecology
- labeling-0.4.2 Axis Labeling
- labelled-2.9.0 Manipulating Labelled Data
- laeken-0.5.2 Estimation of Indicators on Social Exclusion and Poverty
- lambda.r-1.2.4 Modeling Data with Functional Programming
- lars-1.2 Least Angle Regression, Lasso and Forward Stagewise
- lasso2-1.2-22 L1 Constrained Estimation aka `lasso’
- lassosum 0.4.5
- latentnet-2.10.5 Latent Position and Cluster Models for Statistical Networks
- later-1.3.0 Utilities for Scheduling Functions to Execute Later with Event Loops
- lattice-0.20-45 Trellis Graphics for R
- latticeExtra-0.6-29 Extra Graphical Utilities Based on Lattice
- lava-1.6.10 Latent Variable Models
- lavaan-0.6-9 Latent Variable Analysis
- lazy-1.2-16 Lazy Learning for Local Regression
- lazyeval-0.2.2 Lazy (Non-Standard) Evaluation
- lda-1.4.2 Collapsed Gibbs Sampling Methods for Topic Models
- leaps-3.1 Regression Subset Selection
- leiden-0.3.9 R Implementation of Leiden Clustering Algorithm
- lhs-1.1.3 Latin Hypercube Samples
- libcoin-1.0-9 Linear Test Statistics for Permutation Inference
- lifecycle-1.0.1 Manage the Life Cycle of your Package Functions
- limSolve-1.5.6 Solving Linear Inverse Models
- limma-3.50.0 Linear Models for Microarray Data
- linkcomm-1.0-14 Tools for Generating, Visualizing, and Analysing Link Communities in Networks
- linprog-0.9-2 Linear Programming / Optimization
- lintr-2.0.1 A ‘Linter’ for R Code
- liquidSVM-1.2.4 A Fast and Versatile SVM Package
- listenv-0.8.0 Environments Behaving (Almost) as Lists
- lme4-1.1-27.1 Linear Mixed-Effects Models using ‘Eigen’ and S4
- lmerTest-3.1-3 Tests in Linear Mixed Effects Models
- lmom-2.8 L-Moments
- lmtest-0.9-38 Testing Linear Regression Models
- lobstr-1.1.1 Visualize R Data Structures with Trees
- locfdr-1.1-8 Computes Local False Discovery Rates
- locfit-1.5-9.4 Local Regression, Likelihood and Density Estimation
- logcondens-2.1.6 Estimate a Log-Concave Probability Density from Iid Observations
- logistf-1.24 Firth’s Bias-Reduced Logistic Regression
- logspline-2.1.16 Routines for Logspline Density Estimation
- lokern-1.1-9 Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
- longitudinal-1.1.12 Analysis of Multiple Time Course Data
- longmemo-1.1-2 Statistics for Long-Memory Processes (Book Jan Beran), and Related Functionality
- loo-2.4.1 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
- lpSolve-5.6.15 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
- lpSolveAPI-5.5.2.0-17.7 R Interface to ‘lp_solve’ Version 5.5.2.0
- lpridge-1.0-8 Local Polynomial (Ridge) Regression
- lpsymphony-1.22.0 Symphony integer linear programming solver in R
- lqa-1.0-3 Penalized Likelihood Inference for GLMs
- lsei-1.3-0 Solving Least Squares or Quadratic Programming Problems under Equality/Inequality Constraints
- lslx-0.6.10 Semi-Confirmatory Structural Equation Modeling via Penalized Likelihood or Least Squares
- lubridate-1.8.0 Make Dealing with Dates a Little Easier
- lumi-2.46.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
- lwgeom-0.2-8 Bindings to Selected ‘liblwgeom’ Functions for Simple Features
- mRMRe-2.1.2 Parallelized Minimum Redundancy, Maximum Relevance (mRMR)
- maSigPro-1.66.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
- magic-1.5-9 Create and Investigate Magic Squares
- magick-2.7.3 Advanced Graphics and Image-Processing in R
- magrittr-2.0.1 A Forward-Pipe Operator for R
- manipulateWidget-0.11.1 Add Even More Interactivity to Interactive Charts
- mapdata-2.3.0 Extra Map Databases
- mapproj-1.2.7 Map Projections
- maps-3.4.0 Draw Geographical Maps
- maptools-1.1-2 Tools for Handling Spatial Objects
- markdown-1.1 Render Markdown with the C Library ‘Sundown’
- marray-1.72.0 Exploratory analysis for two-color spotted microarray data
- mathjaxr-1.4-0 Using ‘Mathjax’ in Rd Files
- matrixStats-0.61.0 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
- matrixcalc-1.0-5 Collection of Functions for Matrix Calculations
- maxLik-1.5-2 Maximum Likelihood Estimation and Related Tools
- maxlike-0.1-8 Model Species Distributions by Estimating the Probability of Occurrence Using Presence-Only Data
- maxnet-0.1.4 Fitting ‘Maxent’ Species Distribution Models with ‘glmnet’
- mboost-2.9-5 Model-Based Boosting
- mclust-5.4.7 Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
- mcmc-0.9-7 Markov Chain Monte Carlo
- mcmcse-1.5-0 Monte Carlo Standard Errors for MCMC
- mda-0.5-2 Mixture and Flexible Discriminant Analysis
- medflex-0.6-7 Flexible Mediation Analysis Using Natural Effect Models
- mediation-4.5.0 Causal Mediation Analysis
- memoise-2.0.0 ‘Memoisation’ of Functions
- memuse-4.2-1 Memory Estimation Utilities
- metafor-3.0-2 Meta-Analysis Package for R
- metagenomeSeq-1.36.0 Statistical analysis for sparse high-throughput sequencing
- methods built in
- methylKit-1.20.0 DNA methylation analysis from high-throughput bisulfite sequencing results
- methylumi-2.40.1 Handle Illumina methylation data
- mets-1.2.9 Analysis of Multivariate Event Times
- mgcv-1.8-38 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
- mgsub-1.7.3 Safe, Multiple, Simultaneous String Substitution
- mhsmm-0.4.16 Inference for Hidden Markov and Semi-Markov Models
- mi-1.0 Missing Data Imputation and Model Checking
- mice-3.13.0 Multivariate Imputation by Chained Equations
- miceadds-3.11-6 Some Additional Multiple Imputation Functions, Especially for ‘mice’
- microbenchmark-1.4.9 Accurate Timing Functions
- mime-0.12 Map Filenames to MIME Types
- minerva-1.5.10 Maximal Information-Based Nonparametric Exploration for Variable Analysis
- minfi-1.40.0 Analyze Illumina Infinium DNA methylation arrays
- miniUI-0.1.1.1 Shiny UI Widgets for Small Screens
- minpack.lm-1.2-1 R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds
- minqa-1.2.4 Derivative-free optimization algorithms by quadratic approximation
- misc3d-0.9-1 Miscellaneous 3D Plots
- miscTools-0.6-26 Miscellaneous Tools and Utilities
- missForest-1.4 Nonparametric Missing Value Imputation using Random Forest
- mitml-0.4-3 Tools for Multiple Imputation in Multilevel Modeling
- mitools-2.4 Tools for Multiple Imputation of Missing Data
- mixOmics-6.18.1 Omics Data Integration Project
- mixsqp-0.3-43 Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
- mixtools-1.2.0 Tools for Analyzing Finite Mixture Models
- mlbench-2.1-3 Machine Learning Benchmark Problems
- mlegp-3.1.8 Maximum Likelihood Estimates of Gaussian Processes
- mlogit-1.1-1 Multinomial Logit Models
- mlr-2.19.0 Machine Learning in R
- mltools-0.3.5 Machine Learning Tools
- mnormt-2.0.2 The Multivariate Normal and t Distributions, and Their Truncated Versions
- modeldata-0.1.1 Data Sets Used Useful for Modeling Packages
- modelr-0.1.8 Modelling Functions that Work with the Pipe
- modeltools-0.2-23 Tools and Classes for Statistical Models
- moments-0.14 Moments, cumulants, skewness, kurtosis and related tests
- mondate-0.10.02 Keep Track of Dates in Terms of Months
- motifmatchr-1.16.0 Fast Motif Matching in R
- mpath-0.4-2.19 Regularized Linear Models
- msa-1.26.0 Multiple Sequence Alignment
- msigdbr-7.4.1 MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
- msm-1.6.9 Multi-State Markov and Hidden Markov Models in Continuous Time
- multcomp-1.4-17 Simultaneous Inference in General Parametric Models
- multicool-0.1-12 Permutations of Multisets in Cool-Lex Order
- multipol-1.0-7 Multivariate Polynomials
- multtest-2.50.0 Resampling-based multiple hypothesis testing
- munsell-0.5.0 Utilities for Using Munsell Colours
- mvabund-4.1.12 Statistical Methods for Analysing Multivariate Abundance Data
- mvnfast-0.2.7 Fast Multivariate Normal and Student’s t Methods
- mvtnorm-1.1-3 Multivariate Normal and t Distributions
- nabor-0.5.0 Wraps ‘libnabo’, a Fast K Nearest Neighbour Library for Low Dimensions
- naniar-0.6.1 Data Structures, Summaries, and Visualisations for Missing Data
- nanotime-0.3.4 Nanosecond-Resolution Time Support for R
- natserv-1.0.0 ‘NatureServe’ Interface
- naturalsort-0.1.3 Natural Ordering
- ncbit-2013.03.29 retrieve and build NBCI taxonomic data
- ncdf4-1.17 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
- ncdfFlow-2.40.0 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
- ndtv-0.13.2 Network Dynamic Temporal Visualizations
- network-1.17.1 Classes for Relational Data
- networkDynamic-0.11.0 Dynamic Extensions for Network Objects
- networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
- neuRosim-0.2-12 Functions to Generate fMRI Data Including Activated Data, Noise Data and Resting State Data
- neuralnet-1.44.2 Training of Neural Networks
- ngspatial-1.2-2 Fitting the Centered Autologistic and Sparse Spatial Generalized Linear Mixed Models for Areal Data
- nleqslv-3.3.2 Solve Systems of Nonlinear Equations
- nlme-3.1-153 Linear and Nonlinear Mixed Effects Models
- nloptr-1.2.2.2 R Interface to NLopt
- nlsem-0.8 Fitting Structural Equation Mixture Models
- nnet-7.3-16 Feed-Forward Neural Networks and Multinomial Log-Linear Models
- nnls-1.4 The Lawson-Hanson algorithm for non-negative least squares (NNLS)
- nonnest2-0.5-5 Tests of Non-Nested Models
- nor1mix-1.3-0 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods)
- norm-1.0-9.5 Analysis of multivariate normal datasets with missing values
- nortest-1.0-4 Tests for Normality
- np-0.60-11 Nonparametric Kernel Smoothing Methods for Mixed Data Types
- npsurv-0.5-0 Nonparametric Survival Analysis
- numDeriv-2016.8-1.1 Accurate Numerical Derivatives
- numbers-0.8-2 Number-Theoretic Functions
- nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
- oai-0.3.2 General Purpose ‘Oai-PMH’ Services Client
- oce-1.4-0 Analysis of Oceanographic Data
- odbc-1.3.2 Connect to ODBC Compatible Databases (using the DBI Interface)
- oddsratio-2.0.1 Odds Ratio Calculation for GAM(M)s & GLM(M)s
- oligo-1.58.0 Preprocessing tools for oligonucleotide arrays
- oligoClasses-1.56.0 Classes for high-throughput arrays supported by oligo and crlmm
- openCyto-2.6.0 Hierarchical Gating Pipeline for flow cytometry data
- openssl-1.4.5 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
- openxlsx-4.2.4 Read, Write and Edit xlsx Files
- operator.tools-1.6.3 Utilities for Working with R’s Operators
- optextras-2019-12.4 Tools to Support Optimization Possibly with Bounds and Masks
- optimr-2019-12.16 A Replacement and Extension of the ‘optim’ Function
- optimx-2021-10.12 Expanded Replacement and Extension of the ‘optim’ Function
- optmatch-0.9-15 Functions for Optimal Matching
- optparse-1.7.1 Command Line Option Parser
- ordinal-2019.12-10 Regression Models for Ordinal Data
- org.Hs.eg.db-3.14.0 Genome wide annotation for Human
- org.Mm.eg.db-3.14.0 Genome wide annotation for Mouse
- origami-1.0.5 Generalized Framework for Cross-Validation
- oro.nifti-0.11.0 Rigorous - ‘NIfTI’ + ‘ANALYZE’ + ‘AFNI’ : Input / Output
- orthopolynom-1.0-5 Collection of functions for orthogonal and orthonormal polynomials
- outliers-0.14 Tests for outliers
- pROC-1.18.0 Display and Analyze ROC Curves
- pack-0.1-1 Convert values to/from raw vectors
- packrat-0.7.0 A Dependency Management System for Projects and their R Package Dependencies
- pacman-0.5.1 Package Management Tool
- pamr-1.56.1 Pam: Prediction Analysis for Microarrays
- pan-1.6 Multiple Imputation for Multivariate Panel or Clustered Data
- parallel built in
- parallelMap-1.5.1 Unified Interface to Parallelization Back-Ends
- parallelly-1.28.1 Enhancing the ‘parallel’ Package
- parsedate-1.2.1 Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats
- parsnip-0.1.7 A Common API to Modeling and Analysis Functions
- partools-1.1.6 Tools for the ‘Parallel’ Package
- party-1.3-9 A Laboratory for Recursive Partytioning
- partykit-1.2-15 A Toolkit for Recursive Partytioning
- pastecs-1.3.21 Package for Analysis of Space-Time Ecological Series
- patchwork-1.1.1 The Composer of Plots
- pathview-1.34.0 a tool set for pathway based data integration and visualization
- pbapply-1.5-0 Adding Progress Bar to ‘apply’ Functions
- pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
- pbkrtest-0.5.1 Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models
- pbs-1.1 Periodic B Splines
- pcaMethods-1.86.0 A collection of PCA methods
- pcaPP-1.9-74 Robust PCA by Projection Pursuit
- pdftools-3.0.1 Text Extraction, Rendering and Converting of PDF Documents
- pdist-1.2 Partitioned Distance Function
- pedigree-1.4 Pedigree functions
- pedigreemm-0.3-3 Pedigree-based mixed-effects models
- penalized-0.9-51 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
- peperr-1.3 Parallelised Estimation of Prediction Error
- perm-1.0-0.2 Exact or Asymptotic Permutation Tests
- permute-0.9-5 Functions for Generating Restricted Permutations of Data
- phangorn-2.7.1 Phylogenetic Reconstruction and Analysis
- pheatmap-1.0.12 Pretty Heatmaps
- phylobase-0.8.10 Base Package for Phylogenetic Structures and Comparative Data
- phyloseq-1.38.0 Handling and analysis of high-throughput microbiome census data
- phytools-0.7-90 Phylogenetic Tools for Comparative Biology (and Other Things)
- pillar-1.6.4 Coloured Formatting for Columns
- pim-2.0.2 Fit Probabilistic Index Models
- pinfsc50-1.2.0 Sequence (‘FASTA’), Annotation (‘GFF’) and Variants (‘VCF’) for 17 Samples of ‘P. Infestans” and 1 ‘P. Mirabilis’
- pixmap-0.4-12 Bitmap Images / Pixel Maps
- pkgbuild-1.2.0 Find Tools Needed to Build R Packages
- pkgconfig-2.0.3 Private Configuration for ‘R’ Packages
- pkgload-1.2.3 Simulate Package Installation and Attach
- pkgmaker-0.32.2 Development Utilities for R Packages
- plogr-0.2.0 The ‘plog’ C++ Logging Library
- plot3D-1.4 Plotting Multi-Dimensional Data
- plot3Drgl-1.0.2 Plotting Multi-Dimensional Data - Using ‘rgl’
- plotly-4.10.0 Create Interactive Web Graphics via ‘plotly.js’
- plotmo-3.6.1 Plot a Model’s Residuals, Response, and Partial Dependence Plots
- plotrix-3.8-2 Various Plotting Functions
- pls-2.8-0 Partial Least Squares and Principal Component Regression
- plyr-1.8.6 Tools for Splitting, Applying and Combining Data
- png-0.1-7 Read and write PNG images
- poLCA-1.4.1 Polytomous variable Latent Class Analysis
- poisbinom-1.0.1 A Faster Implementation of the Poisson-Binomial Distribution
- polspline-1.1.19 Polynomial Spline Routines
- polyclip-1.10-0 Polygon Clipping
- polycor-0.7-10 Polychoric and Polyserial Correlations
- polyester-1.30.0 Simulate RNA-seq reads
- polynom-1.4-0 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
- posterior-1.1.0 Tools for Working with Posterior Distributions
- poweRlaw-0.70.6 Analysis of Heavy Tailed Distributions
- prabclus-2.3-2 Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data
- pracma-2.3.3 Practical Numerical Math Functions
- praise-1.0.0 Praise Users
- premessa 0.2.6
- preprocessCore-1.56.0 A collection of pre-processing functions
- preseqR-4.0.0 Predicting Species Accumulation Curves
- prettyunits-1.1.1 Pretty, Human Readable Formatting of Quantities
- processx-3.5.2 Execute and Control System Processes
- prodlim-2019.11.13 Product-Limit Estimation for Censored Event History Analysis
- profileModel-0.6.1 Profiling Inference Functions for Various Model Classes
- proftools-0.99-3 Profile Output Processing Tools for R
- progress-1.2.2 Terminal Progress Bars
- progressr-0.9.0 An Inclusive, Unifying API for Progress Updates
- projpred-2.0.2 Projection Predictive Feature Selection
- promises-1.2.0.1 Abstractions for Promise-Based Asynchronous Programming
- proto-1.0.0 Prototype Object-Based Programming
- proxy-0.4-26 Distance and Similarity Measures
- pryr-0.1.5 Tools for Computing on the Language
- ps-1.6.0 List, Query, Manipulate System Processes
- pscl-1.5.5 Political Science Computational Laboratory
- pspline-1.0-18 Penalized Smoothing Splines
- psych-2.1.9 Procedures for Psychological, Psychometric, and Personality Research
- psychotools-0.7-0 Psychometric Modeling Infrastructure
- pulsar-0.3.7 Parallel Utilities for Lambda Selection along a Regularization Path
- purrr-0.3.4 Functional Programming Tools
- pvclust-2.2-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
- qdapRegex-0.7.2 Regular Expression Removal, Extraction, and Replacement Tools
- qgam-1.3.3 Smooth Additive Quantile Regression Models
- qgraph-1.9 Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
- qpdf-1.1 Split, Combine and Compress PDF Files
- qqman-0.1.8 Q-Q and Manhattan Plots for GWAS Data
- qrnn-2.0.5 Quantile Regression Neural Network
- qtl-1.50 Tools for Analyzing QTL Experiments
- quadprog-1.5-8 Functions to Solve Quadratic Programming Problems
- quantmod-0.4.18 Quantitative Financial Modelling Framework
- quantoptr-0.1.3 Algorithms for Quantile- And Mean-Optimal Treatment Regimes
- quantreg-5.86 Quantile Regression
- quantsmooth-1.60.0 Quantile smoothing and genomic visualization of array data
- questionr-0.7.5 Functions to Make Surveys Processing Easier
- qvalue-2.26.0 Q-value estimation for false discovery rate control
- qvcalc-1.0.2 Quasi Variances for Factor Effects in Statistical Models
- r2d3-0.2.5 Interface to ‘D3’ Visualizations
- rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
- rGADEM-2.42.0 de novo motif discovery
- rJava-1.0-5 Low-Level R to Java Interface
- rainbow-3.6 Bagplots, Boxplots and Rainbow Plots for Functional Data
- randomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and Regression
- randomForestSRC-2.13.0 Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
- rangeModelMetadata-0.1.4 Provides Templates for Metadata Files Associated with Species Range Models
- ranger-0.13.1 A Fast Implementation of Random Forests
- rappdirs-0.3.3 Application Directories: Determine Where to Save Data, Caches, and Logs
- raster-3.5-2 Geographic Data Analysis and Modeling
- rasterVis-0.51.0 Visualization Methods for Raster Data
- ratelimitr-0.4.1 Rate Limiting for R
- rbenchmark-1.0.0 Benchmarking routine for R
- rbibutils-2.2.4 Read ‘Bibtex’ Files and Convert Between Bibliography Formats
- rbison-1.0.0 Interface to the ‘USGS’ ‘BISON’ API
- rcmdcheck-1.4.0 Run ‘R CMD check’ from ‘R’ and Capture Results
- rda-1.0.2-2.1 Shrunken Centroids Regularized Discriminant Analysis
- rdrop2-0.8.2.1 Programmatic Interface to the ‘Dropbox’ API
- readODS-1.7.0 Read and Write ODS Files
- readbitmap-0.1.5 Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF)
- reader-1.0.6 Suite of Functions to Flexibly Read Data from Files
- readr-2.0.2 Read Rectangular Text Data
- readxl-1.3.1 Read Excel Files
- rebird-1.3.0 R Client for the eBird Database of Bird Observations
- recipes-0.1.17 Preprocessing and Feature Engineering Steps for Modeling
- refGenome-1.7.7 Gene and Splice Site Annotation Using Annotation Data from ‘Ensembl’ and ‘UCSC’ Genome Browsers
- refund-0.1-24 Regression with Functional Data
- regioneR-1.26.0 Association analysis of genomic regions based on permutation tests
- registry-0.5-1 Infrastructure for R Package Registries
- regress-1.3-21 Gaussian Linear Models with Linear Covariance Structure
- regsem-1.8.0 Regularized Structural Equation Modeling
- regtools-1.1.0 Regression and Classification Tools
- relations-0.6-10 Data Structures and Algorithms for Relations
- relevent-1.1 Relational Event Models
- rematch-1.0.1 Match Regular Expressions with a Nicer ‘API’
- rematch2-2.1.2 Tidy Output from Regular Expression Matching
- remotes-2.4.1 R Package Installation from Remote Repositories, Including ‘GitHub’
- rentrez-1.2.3 ‘Entrez’ in R
- repr-1.1.3 Serializable Representations
- reprex-2.0.1 Prepare Reproducible Example Code via the Clipboard
- resample-0.4 Resampling Functions
- reshape-0.8.8 Flexibly Reshape Data
- reshape2-1.4.4 Flexibly Reshape Data: A Reboot of the Reshape Package
- restfulr-0.0.13 R Interface to RESTful Web Services
- reticulate-1.22 Interface to ‘Python’
- rex-1.2.0 Friendly Regular Expressions
- rgbif-3.6.0 Interface to the Global ‘Biodiversity’ Information Facility API
- rgdal-1.5-27 Bindings for the ‘Geospatial’ Data Abstraction Library
- rgenoud-5.8-3.0 R Version of GENetic Optimization Using Derivatives
- rgeos-0.5-8 Interface to Geometry Engine - Open Source (‘GEOS’)
- rgexf-0.16.2 Build, Import and Export GEXF Graph Files
- rgl-0.107.14 3D Visualization Using OpenGL
- rhandsontable-0.3.8 Interface to the ‘Handsontable.js’ Library
- rhdf5-2.38.0 R Interface to HDF5
- rhdf5filters-1.6.0 HDF5 Compression Filters
- ridigbio-0.3.5 Interface to the iDigBio Data API
- rio-0.5.27 A Swiss-Army Knife for Data I/O
- ritis-1.0.0 Integrated Taxonomic Information System Client
- rjags-4-12 Bayesian Graphical Models using MCMC
- rjson-0.2.20 JSON for R
- rlang-0.4.12 Functions for Base Types and Core R and ‘Tidyverse’ Features
- rle-0.9.2 Common Functions for Run-Length Encoded Vectors
- rlecuyer-0.3-5 R Interface to RNG with Multiple Streams
- rlist-0.4.6.2 A Toolbox for Non-Tabular Data Manipulation
- rmarkdown-2.11 Dynamic Documents for R
- rmeta-3.0 Meta-Analysis
- rms-6.2-0 Regression Modeling Strategies
- rncl-0.8.4 An Interface to the Nexus Class Library
- rnetcarto-0.2.4 Fast Network Modularity and Roles Computation by Simulated Annealing (Rgraph C Library Wrapper for R)
- rngtools-1.5.2 Utility Functions for Working with Random Number Generators
- robustbase-0.93-9 Basic Robust Statistics
- rootSolve-1.8.2.3 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
- rotl-3.0.11 Interface to the ‘Open Tree of Life’ API
- roxygen2-7.1.2 In-Line Documentation for R
- rpart-4.1-15 Recursive Partitioning and Regression Trees
- rprojroot-2.0.2 Finding Files in Project Subdirectories
- rrcov-1.6-0 Scalable Robust Estimators with High Breakdown Point
- rredlist-0.7.0 ‘IUCN’ Red List Client
- rsample-0.1.1 General Resampling Infrastructure
- rsconnect-0.8.24 Deployment Interface for R Markdown Documents and Shiny Applications
- rslurm-0.6.1 Submit R Calculations to a ‘Slurm’ Cluster
- rstan-2.21.2 R Interface to Stan
- rstanarm-2.21.1 Bayesian Applied Regression Modeling via Stan
- rstantools-2.1.1 Tools for Developing R Packages Interfacing with ‘Stan’
- rstatix-0.7.0 Pipe-Friendly Framework for Basic Statistical Tests
- rstudioapi-0.13 Safely Access the RStudio API
- rsvd-1.0.5 Randomized Singular Value Decomposition
- rsvg-2.1.2 Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
- rtracklayer-1.54.0 R interface to genome annotation files and the UCSC genome browser
- ruv-0.9.7.1 Detect and Remove Unwanted Variation using Negative Controls
- rvcheck-0.2.1 R/Package Version Check
- rversions-2.1.1 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
- rvertnet-0.8.2 Search ‘Vertnet’, a ‘Database’ of Vertebrate Specimen Records
- rvest-1.0.2 Easily Harvest (Scrape) Web Pages
- rzmq-0.9.8 R Bindings for ‘ZeroMQ’
- s2-1.0.7 Spherical Geometry Operators Using the S2 Geometry Library
- sampling-2.9 Survey Sampling
- samr-3.0 SAM: Significance Analysis of Microarrays
- sandwich-3.0-1 Robust Covariance Matrix Estimators
- sass-0.4.0 Syntactically Awesome Style Sheets (‘Sass’)
- scales-1.1.1 Scale Functions for Visualization
- scater-1.22.0 Single-Cell Analysis Toolkit for Gene Expression Data in R
- scattermore-0.7 Scatterplots with More Points
- scatterpie-0.1.7 Scatter Pie Plot
- scatterplot3d-0.3-41 3D Scatter Plot
- schoolmath-0.4 Functions and datasets for math used in school
- scidb-3.0.0 An R Interface to SciDB
- scrime-1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
- sctransform-0.3.2 Variance Stabilizing Transformations for Single Cell UMI Data
- scuttle-1.4.0 Single-Cell RNA-Seq Analysis Utilities
- seewave-2.1.8 Sound Analysis and Synthesis
- segmented-1.3-4 Regression Models with Break-Points / Change-Points Estimation
- selectr-0.4-2 Translate CSS Selectors to XPath Expressions
- sem-3.1-13 Structural Equation Models
- semPLS-1.0-10 Structural Equation Modeling Using Partial Least Squares
- sendmailR-1.2-1 send email using R
- sensemakr-0.1.4 Sensitivity Analysis Tools for Regression Models
- seqLogo-1.60.0 Sequence logos for DNA sequence alignments
- seqinr-4.2-8 Biological Sequences Retrieval and Analysis
- seqminer-8.2 Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
- sequenza-3.0.0 Copy Number Estimation from Tumor Genome Sequencing Data
- servr-0.23 A Simple HTTP Server to Serve Static Files or Dynamic Documents
- sessioninfo-1.2.0 R Session Information
- setRNG-2013.9-1 Set (Normal) Random Number Generator and Seed
- sets-1.0-19 Sets, Generalized Sets, Customizable Sets and Intervals
- sf-1.0-3 Simple Features for R
- sfsmisc-1.1-12 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
- shadowtext-0.0.9 Shadow Text Grob and Layer
- shape-1.4.6 Functions for Plotting Graphical Shapes, Colors
- shapefiles-0.7 Read and Write ESRI Shapefiles
- shiny-1.7.1 Web Application Framework for R
- shinyBS-0.61 Twitter Bootstrap Components for Shiny
- shinyFiles-0.9.1 A Server-Side File System Viewer for Shiny
- shinycssloaders-1.0.0 Add Loading Animations to a ‘shiny’ Output While It’s Recalculating
- shinydashboard-0.7.2 Create Dashboards with ‘Shiny’
- shinyjs-2.0.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
- shinystan-2.5.0 Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
- shinythemes-1.2.0 Themes for Shiny
- siggenes-1.68.0 Multiple Testing using SAM and Efron’s Empirical Bayes Approaches
- signal-0.7-7 Signal Processing
- sitmo-2.0.2 Parallel Pseudo Random Number Generator (PPRNG) ‘sitmo’ Header Files
- slam-0.1-48 Sparse Lightweight Arrays and Matrices
- slider-0.2.2 Sliding Window Functions
- sm-2.2-5.7 Smoothing Methods for Nonparametric Regression and Density Estimation
- smoother-1.1 Functions Relating to the Smoothing of Numerical Data
- sn-2.0.0 The Skew-Normal and Related Distributions Such as the Skew-t and the SUN
- sna-2.6 Tools for Social Network Analysis
- snow-0.4-4 Simple Network of Workstations
- snowfall-1.84-6.1 Easier cluster computing (based on snow).
- snpStats-1.44.0 SnpMatrix and XSnpMatrix classes and methods
- sodium-1.2.0 A Modern and Easy-to-Use Crypto Library
- solrium-1.2.0 General Purpose R Interface to ‘Solr’
- som-0.3-5.1 Self-Organizing Map
- soundecology-1.3.3 Soundscape Ecology
- sourcetools-0.1.7 Tools for Reading, Tokenizing and Parsing R Code
- sp-1.4-5 Classes and Methods for Spatial Data
- spData-2.0.1 Datasets for Spatial Analysis
- spThin-0.2.0 Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models
- spaMM-3.9.13 Mixed-Effect Models, with or without Spatial Random Effects
- spaa-0.2.2 SPecies Association Analysis
- spam-2.7-0 SPArse Matrix
- sparklyr-1.7.2 R Interface to Apache Spark
- sparseMatrixStats-1.6.0 Summary Statistics for Rows and Columns of Sparse Matrices
- spatial-7.3-14 Functions for Kriging and Point Pattern Analysis
- spatstat-2.2-0 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
- spatstat.core-2.3-0 Core Functionality of the ‘spatstat’ Family
- spatstat.data-2.1-0 Datasets for ‘spatstat’ Family
- spatstat.geom-2.3-0 Geometrical Functionality of the ‘spatstat’ Family
- spatstat.linnet-2.3-0 Linear Networks Functionality of the ‘spatstat’ Family
- spatstat.sparse-2.0-0 Sparse Three-Dimensional Arrays and Linear Algebra Utilities
- spatstat.utils-2.2-0 Utility Functions for ‘spatstat’
- splines built in
- splitstackshape-1.4.8 Stack and Reshape Datasets After Splitting Concatenated Values
- spls-2.2-3 Sparse Partial Least Squares (SPLS) Regression and Classification
- spocc-1.2.0 Interface to Species Occurrence Data Sources
- sqldf-0.4-11 Manipulate R Data Frames Using SQL
- squash-1.0.9 Color-Based Plots for Multivariate Visualization
- ssgraph-1.12 Bayesian Graphical Estimation using Spike-and-Slab Priors
- stabledist-0.7-1 Stable Distribution Functions
- stabs-0.6-4 Stability Selection with Error Control
- stargazer-5.2.2 Well-Formatted Regression and Summary Statistics Tables
- startupmsg-0.9.6 Utilities for Start-Up Messages
- statmod-1.4.36 Statistical Modeling
- statnet-2019.6 Software Tools for the Statistical Analysis of Network Data
- statnet.common-4.5.0 Common R Scripts and Utilities Used by the Statnet Project Software
- stats built in
- stats4 built in
- stdReg-3.4.1 Regression Standardization
- stopwords-2.3 Multilingual Stopword Lists
- stringdist-0.9.8 Approximate String Matching, Fuzzy Text Search, and String Distance Functions
- stringi-1.7.5 Character String Processing Facilities
- stringr-1.4.0 Simple, Consistent Wrappers for Common String Operations
- strucchange-1.5-2 Testing, Monitoring, and Dating Structural Changes
- styler-1.6.2 Non-Invasive Pretty Printing of R Code
- subplex-1.6 Unconstrained Optimization using the Subplex Algorithm
- survey-4.1-1 Analysis of Complex Survey Samples
- survival-3.2-13 Survival Analysis
- survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
- sva-3.42.0 Surrogate Variable Analysis
- svd-0.5 Interfaces to Various State-of-Art SVD and Eigensolvers
- symmoments-1.2.1 Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution
- sys-3.4 Powerful and Reliable Tools for Running System Commands in R
- systemPipeR-2.0.1 systemPipeR: NGS workflow and report generation environment
- systemfonts-1.0.3 System Native Font Finding
- tableone-0.13.0 Create ‘Table 1’ to Describe Baseline Characteristics with or without Propensity Score Weights
- tables-0.9.6 Formula-Driven Table Generation
- taxize-0.9.99 Taxonomic Information from Around the Web
- tcltk built in
- tcltk2-1.2-11 Tcl/Tk Additions
- tclust-1.4-2 Robust Trimmed Clustering
- tensor-1.5 Tensor product of arrays
- tensorA-0.36.2 Advanced Tensor Arithmetic with Named Indices
- tergm-4.0.2 Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
- tergmLite-2.5.5 Fast Simulation of Simple Temporal Exponential Random Graph Models
- terra-1.4-11 Spatial Data Analysis
- testit-0.13 A Simple Package for Testing R Packages
- testthat-3.1.0 Unit Testing for R
- threejs-0.3.3 Interactive 3D Scatter Plots, Networks and Globes
- tibble-3.1.5 Simple Data Frames
- tictoc-1.0.1 Functions for Timing R Scripts, as Well as Implementations of Stack and List Structures
- tidygraph-1.2.0 A Tidy API for Graph Manipulation
- tidymodels-0.1.4 Easily Install and Load the ‘Tidymodels’ Packages
- tidyposterior-0.1.0 Bayesian Analysis to Compare Models using Resampling Statistics
- tidypredict-0.4.8 Run Predictions Inside the Database
- tidyr-1.1.4 Tidy Messy Data
- tidyselect-1.1.1 Select from a Set of Strings
- tidytext-0.3.2 Text Mining using ‘dplyr’, ‘ggplot2’, and Other Tidy Tools
- tidytree-0.3.6 A Tidy Tool for Phylogenetic Tree Data Manipulation
- tidyverse-1.3.1 Easily Install and Load the ‘Tidyverse’
- tiff-0.1-8 Read and Write TIFF Images
- tilingArray-1.72.0 Transcript mapping with high-density oligonucleotide tiling arrays
- timeDate-3043.102 Rmetrics - Chronological and Calendar Objects
- timeSeries-3062.100 Financial Time Series Objects (Rmetrics)
- timereg-2.0.1 Flexible Regression Models for Survival Data
- tinytex-0.34 Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
- tkWidgets-1.72.0 R based tk widgets
- tkrplot-0.0-26 TK Rplot
- tm-0.7-8 Text Mining Package
- tmle-1.5.0.2 Targeted Maximum Likelihood Estimation
- tmvnsim-1.0-2 Truncated Multivariate Normal Simulation
- tmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distribution
- tokenizers-0.2.1 Fast, Consistent Tokenization of Natural Language Text
- tools built in
- topicmodels-0.2-12 Topic Models
- tree-1.0-41 Classification and Regression Trees
- treeio-1.18.1 Base Classes and Functions for Phylogenetic Tree Input and Output
- triebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’
- trimcluster-0.1-5 Cluster Analysis with Trimming
- tripack-1.3-9.1 Triangulation of Irregularly Spaced Data
- truncnorm-1.0-8 Truncated Normal Distribution
- trust-0.1-8 Trust Region Optimization
- tseries-0.10-48 Time Series Analysis and Computational Finance
- tseriesChaos-0.1-13.1 Analysis of Nonlinear Time Series
- tsna-0.3.4 Tools for Temporal Social Network Analysis
- tsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
- tune-0.1.6 Tidy Tuning Tools
- tuneR-1.3.3.1 Analysis of Music and Speech
- twang-2.5 Toolkit for Weighting and Analysis of Nonequivalent Groups
- tweedie-2.3.3 Evaluation of Tweedie Exponential Family Models
- tweenr-1.0.2 Interpolate Data for Smooth Animations
- tzdb-0.2.0 Time Zone Database Information
- ucminf-1.1-4 General-Purpose Unconstrained Non-Linear Optimization
- udunits2-0.13.1 Udunits-2 Bindings for R
- unbalanced-2.0 Racing for Unbalanced Methods Selection
- uniqueAtomMat-0.1-3-2 Finding Unique or Duplicated Rows or Columns for Atomic Matrices
- units-0.7-2 Measurement Units for R Vectors
- unmarked-1.1.1 Models for Data from Unmarked Animals
- urca-1.3-0 Unit Root and Cointegration Tests for Time Series Data
- urltools-1.7.3 Vectorised Tools for URL Handling and Parsing
- uroot-2.1-2 Unit Root Tests for Seasonal Time Series
- usethis-2.1.3 Automate Package and Project Setup
- utf8-1.2.2 Unicode Text Processing
- utils built in
- uuid-1.0-2 Tools for Generating and Handling of UUIDs
- uwot-0.1.10 The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
- vcd-1.4-9 Visualizing Categorical Data
- vcfR-1.12.0 Manipulate and Visualize VCF Data
- vctrs-0.3.8 Vector Helpers
- vegan-2.5-7 Community Ecology Package
- venn-1.10 Draw Venn Diagrams
- vimp-2.2.5 Perform Inference on Algorithm-Agnostic Variable Importance
- vioplot-0.3.7 Violin Plot
- vipor-0.4.5 Plot Categorical Data Using Quasirandom Noise and Density Estimates
- viridis-0.6.2 Colorblind-Friendly Color Maps for R
- viridisLite-0.4.0 Colorblind-Friendly Color Maps (Lite Version)
- visNetwork-2.1.0 Network Visualization using ‘vis.js’ Library
- visdat-0.5.3 Preliminary Visualisation of Data
- vroom-1.5.5 Read and Write Rectangular Text Data Quickly
- vsn-3.62.0 Variance stabilization and calibration for microarray data
- waldo-0.3.1 Find Differences Between R Objects
- warp-0.2.0 Group Dates
- waveslim-1.8.2 Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing
- wavethresh-4.6.8 Wavelets Statistics and Transforms
- webp-1.1.0 A New Format for Lossless and Lossy Image Compression
- webshot-0.5.2 Take Screenshots of Web Pages
- wellknown-0.7.4 Convert Between ‘WKT’ and ‘GeoJSON’
- whisker-0.4 for R, Logicless Templating
- widgetTools-1.72.0 Creates an interactive tcltk widget
- wikitaxa-0.4.0 Taxonomic Information from ‘Wikipedia’
- withr-2.4.2 Run Code ‘With’ Temporarily Modified Global State
- wk-0.5.0 Lightweight Well-Known Geometry Parsing
- wordcloud-2.6 Word Clouds
- workflows-0.2.4 Modeling Workflows
- workflowsets-0.1.0 Create a Collection of ‘tidymodels’ Workflows
- worrms-0.4.2 World Register of Marine Species (WoRMS) Client
- xCell 1.1.0
- xfun-0.27 Supporting Functions for Packages Maintained by ‘Yihui Xie’
- xgboost-1.4.1.1 Extreme Gradient Boosting
- xlsx-0.6.5 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
- xlsxjars-0.6.1 Package required POI jars for the xlsx package
- xml2-1.3.2 Parse XML
- xmlparsedata-1.0.5 Parse Data of ‘R’ Code as an ‘XML’ Tree
- xopen-1.0.0 Open System Files, ‘URLs’, Anything
- xtable-1.8-4 Export Tables to LaTeX or HTML
- xts-0.12.1 eXtensible Time Series
- yaImpute-1.0-32 Nearest Neighbor Observation Imputation and Evaluation Tools
- yaml-2.2.1 Methods to Convert R Data to YAML and Back
- yardstick-0.0.9 Tidy Characterizations of Model Performance
- yulab.utils-0.0.4 Supporting Functions for Packages Maintained by ‘YuLab-SMU’
- zCompositions-1.3.4 Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
- zeallot-0.1.0 Multiple, Unpacking, and Destructuring Assignment
- zip-2.2.0 Cross-Platform ‘zip’ Compression
- zlibbioc-1.40.0 An R packaged zlib-1.2.5
- zoo-1.8-9 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)