Known Issues
None
Package List
ADGofTest-0.3 Anderson-Darling GoF test
ALDEx2-1.14.1 Analysis Of Differential Abundance Taking Sample Variation Into Account
ASCAT 2.5.2
AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.
AgiMicroRna-2.32.0 Processing and Differential Expression Analysis of Agilent microRNA chips
AlgDesign-1.1-7.3 Algorithmic Experimental Design
AnnotationDbi-1.44.0 Annotation Database Interface
AnnotationFilter-1.6.0 Facilities for Filtering Bioconductor Annotation Resources
AnnotationForge-1.24.0 Code for Building Annotation Database Packages
AnnotationHub-2.14.4 Client to access AnnotationHub resources
BB-2014.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
BBmisc-1.11 Miscellaneous Helper Functions for B. Bischl
BDgraph-2.53 Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
BH-1.66.0-1 Boost C++ Header Files
BSgenome-1.50.0 Software infrastructure for efficient representation of full genomes and their SNPs
BSgenome.Hsapiens.UCSC.hg19-1.4.0 Full genome sequences for Homo sapiens (UCSC version hg19)
BatchJobs-1.7 Batch Computing with R
BayesianTools-0.1.5 General-Purpose MCMC and SMC Samplers and Tools for Bayesian
Statistics
Bhat-0.9-10 General likelihood exploration
BiasedUrn-1.07 Biased Urn Model Distributions
Biobase-2.42.0 Biobase: Base functions for Bioconductor
BiocGenerics-0.28.0 S4 generic functions for Bioconductor
BiocInstaller-1.32.1 Install/Update Bioconductor, CRAN, and github Packages
BiocManager-1.30.4 Access the Bioconductor Project Package Repository
BiocParallel-1.16.6 Bioconductor facilities for parallel evaluation
Biostrings-2.50.2 Efficient manipulation of biological strings
BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
Bolstad-0.2-40 Functions for Elementary Bayesian Inference
Bolstad2-1.0-28 Bolstad functions
BradleyTerry2-1.0-9 Bradley-Terry Models
Brobdingnag-1.2-6 Very Large Numbers in R
CGEN-3.18.0 An R package for analysis of case-control studies in genetic epidemiology
CGHbase-1.42.0 CGHbase: Base functions and classes for arrayCGH data analysis.
CVST-0.2-2 Fast Cross-Validation via Sequential Testing
Cairo-1.5-9 R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) Output
Category-2.48.1 Category Analysis
ComICS-1.0.4 Computational Methods for Immune Cell-Type Subsets
CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
DAAG-1.22.1 Data Analysis and Graphics Data and Functions
DBI-1.0.0 R Database Interface
DEGseq-1.36.1 Identify Differentially Expressed Genes from RNA-seq data
DESeq-1.34.1 Differential gene expression analysis based on the negative binomial distribution
DESeq2-1.22.2 Differential gene expression analysis based on the negative binomial distribution
DEoptimR-1.0-8 Differential Evolution Optimization in Pure R
DHARMa-0.2.0 Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
DNAcopy-1.56.0 DNA copy number data analysis
DRR-0.0.3 Dimensionality Reduction via Regression
DT-0.5 A Wrapper of the JavaScript Library ‘DataTables’
DTRreg-1.3 DTR Estimation and Inference via G-Estimation, Dynamic WOLS, and
Q-Learning
DelayedArray-0.8.0 Delayed operations on array-like objects
DelayedMatrixStats-1.4.0 Functions that Apply to Rows and Columns of ‘DelayedMatrix’ Objects
Deriv-3.8.5 Symbolic Differentiation
DiagrammeR-1.0.0 Graph/Network Visualization
DiffBind-2.10.0 Differential Binding Analysis of ChIP-Seq Peak Data
DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
DistributionUtils-0.6-0 Distribution Utilities
DynDoc-1.60.0 Dynamic document tools
EBImage-4.24.0 Image processing and analysis toolbox for R
EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
EpiModel-1.7.2 Mathematical Modeling of Infectious Disease Dynamics
FDb.InfiniumMethylation.hg19-2.2.0 Annotation package for Illumina Infinium DNA methylation probes
FME-1.3.5 A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo Analysis
FNN-1.1.2.2 Fast Nearest Neighbor Search Algorithms and Applications
FactoMineR-1.41 Multivariate Exploratory Data Analysis and Data Mining
Formula-1.2-3 Extended Model Formulas
GENESIS-2.12.4 GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GEOquery-2.50.5 Get data from NCBI Gene Expression Omnibus (GEO)
GGally-1.4.0 Extension to ‘ggplot2’
GO.db-3.7.0 A set of annotation maps describing the entire Gene Ontology
GOstats-2.48.0 Tools for manipulating GO and microarrays
GSA-1.03 Gene Set Analysis
GSEABase-1.44.0 Gene set enrichment data structures and methods
GUTS-1.1.0 Fast Calculation of the Likelihood of a Stochastic Survival
Model
GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
GenSA-1.1.7 Generalized Simulated Annealing
GeneNet-1.2.13 Modeling and Inferring Gene Networks
GenomeGraphs-1.42.0 Plotting genomic information from Ensembl
GenomeInfoDb-1.18.2 Utilities for manipulating chromosome and other ‘seqname’ identifiers
GenomeInfoDbData-1.2.0 Species and taxonomy ID look up tables used by GenomeInfoDb
GenomicAlignments-1.18.1 Representation and manipulation of short genomic alignments
GenomicFeatures-1.34.4 Tools for making and manipulating transcript centric annotations
GenomicFiles-1.18.0 Distributed computing by file or by range
GenomicRanges-1.34.0 Representation and manipulation of genomic intervals and variables defined along a genome
GetoptLong-0.1.7 Parsing Command-Line Arguments and Variable Interpolation
GillespieSSA-0.5-4 Gillespie’s Stochastic Simulation Algorithm (SSA)
GlobalOptions-0.1.0 Generate Functions to Get or Set Global Options
Gviz-1.26.5 Plotting data and annotation information along genomic coordinates
HCsnip 1.16.0
HDF5Array-1.10.1 HDF5 backend for DelayedArray objects
HMMcopy-1.24.0 Copy number prediction with correction for GC and mappability bias for HTS data
HWxtest-1.1.7 Exact Tests for Hardy-Weinberg Proportions
HaploSim-1.8.4 Functions to simulate haplotypes
Hmisc-4.1-1 Harrell Miscellaneous
Homo.sapiens-1.3.1 Annotation package for the Homo.sapiens object
IDPmisc-1.1.18 ‘Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)’
IRanges-2.16.0 Infrastructure for manipulating intervals on sequences
IRdisplay-0.7.0 ‘Jupyter’ Display Machinery
IlluminaHumanMethylation450kmanifest-0.4.0 Annotation for Illumina’s 450k methylation arrays
Iso-0.0-17 Functions to Perform Isotonic Regression
JBTools-0.7.2.9 Misc Small Tools and Helper Functions for Other Code of J.
Buttlar
KEGG.db-3.2.3 A set of annotation maps for KEGG
KEGGREST-1.22.0 Client-side REST access to KEGG
KEGGgraph-1.42.0 KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGprofile-1.24.0 An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
KODAMA-1.5 Knowledge Discovery by Accuracy Maximization
KernSmooth-2.23-15 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
LearnBayes-2.15.1 Functions for Learning Bayesian Inference
Lmoments-1.2-3 L-Moments and Quantile Mixtures
LogicReg-1.5.10 Logic Regression
LymphoSeq-1.10.0 Analyze high-throughput sequencing of T and B cell receptors
LymphoSeqDB-0.99.2 LymphoSeq annotation databases
MASS-7.3-51.1 Support Functions and Datasets for Venables and Ripley’s MASS
MCMCglmm-2.28 MCMC Generalised Linear Mixed Models
MCMCpack-1.4-4 Markov Chain Monte Carlo (MCMC) Package
MPV-1.53 Data Sets from Montgomery, Peck and Vining
MatchIt-3.0.2 Nonparametric Preprocessing for Parametric Causal Inference
Matching-4.9-3 Multivariate and Propensity Score Matching with Balance
Optimization
Matrix-1.2-15 Sparse and Dense Matrix Classes and Methods
MatrixModels-0.4-1 Modelling with Sparse And Dense Matrices
Mfuzz-2.42.0 Soft clustering of time series gene expression data
ModelMetrics-1.2.2 Rapid Calculation of Model Metrics
MotIV-1.38.0 Motif Identification and Validation
NLP-0.2-0 Natural Language Processing Infrastructure
NMF-0.21.0 Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)
NOISeq-2.26.1 Exploratory analysis and differential expression for RNA-seq data
OceanView-1.0.4 Visualisation of Oceanographic Data and Model Output
OrganismDbi-1.24.0 Software to enable the smooth interfacing of different database packages
PBSddesolve-1.12.4 Solver for Delay Differential Equations
PFAM.db-3.7.0 A set of protein ID mappings for PFAM
PICS-2.26.0 Probabilistic inference of ChIP-seq
ParamHelpers-1.11 Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
PoissonSeq-1.1.2 Significance analysis of sequencing data based on a Poisson log
linear model
PolynomF-1.0-2 Polynomials in R
PresenceAbsence-1.1.9 Presence-Absence Model Evaluation.
ProtGenerics-1.14.0 S4 generic functions for Bioconductor proteomics infrastructure
R.cache-0.13.0 Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up Computations
R.matlab-3.6.2 Read and Write MAT Files and Call MATLAB from Within R
R.methodsS3-1.7.1 S3 Methods Simplified
R.oo-1.22.0 R Object-Oriented Programming with or without References
R.rsp-0.43.0 Dynamic Generation of Scientific Reports
R.utils-2.7.0 Various Programming Utilities
R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
R2jags-0.5-7 Using R to Run ‘JAGS’
R6-2.3.0 Encapsulated Classes with Reference Semantics
RANN-2.6 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
Metric
RBGL-1.58.1 An interface to the BOOST graph library
RCircos-1.2.0 Circos 2D Track Plot
RColorBrewer-1.1-2 ColorBrewer Palettes
RCurl-1.95-4.11 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-0.2.14 C++ Classes to Embed R in C++ Applications
RItools-0.1-16 Randomization Inference Tools
RJSONIO-1.3-1.1 Serialize R Objects to JSON, JavaScript Object Notation
RLRsim-3.1-3 Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models
RMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>Theory
RMySQL-0.10.17 Database Interface and ‘MySQL’ Driver for R
RNASeqPower-1.22.1 Sample size for RNAseq studies
RNeXML-2.2.0 Semantically Rich I/O for the ‘NeXML’ Format
ROCR-1.0-7 Visualizing the Performance of Scoring Classifiers
RPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database System
RProtoBufLib-1.4.0 C++ headers and static libraries of Protocol buffers
RSNNS-0.4-11 Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)
RSQLite-2.1.1 ‘SQLite’ Interface for R
RSpectra-0.13-1 Solvers for Large-Scale Eigenvalue and SVD Problems
RUnit-0.4.32 R Unit Test Framework
RWeka-0.4-39 R/Weka Interface
RWekajars-3.9.3-1 R/Weka Interface Jars
Rcpp-1.0.0 Seamless R and C++ Integration
RcppArmadillo-0.9.200.5.0 ‘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-4.4.2 Parallel Programming Tools for ‘Rcpp’
RcppProgress-0.4.1 An Interruptible Progress Bar with OpenMP Support for C++ in R
Packages
RcppRoll-0.3.0 Efficient Rolling / Windowed Operations
Rdpack-0.10-1 Update and Manipulate Rd Documentation Objects
ReportingTools-2.22.1 Tools for making reports in various formats
Rglpk-0.6-4 R/GNU Linear Programming Kit Interface
Rgraphviz-2.26.0 Provides plotting capabilities for R graph objects
Rhdf5lib-1.4.2 hdf5 library as an R package
Rhpc-0.18-204 Permits *apply() Style Dispatch for ‘HPC’
Ringo-1.46.0 R Investigation of ChIP-chip Oligoarrays
Rlabkey-2.2.4 Data Exchange Between R and ‘LabKey’ Server
Rmpi-0.6-9 Interface (Wrapper) to MPI (Message-Passing Interface)
Rook-1.1-1 Rook - a web server interface for R
Rsamtools-1.34.1 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Rssa-1.0 A Collection of Methods for Singular Spectrum Analysis
Rsubread-1.32.4 Subread sequence alignment and counting for R
Rtsne-0.15 T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
Implementation
Rttf2pt1-1.3.7 ‘ttf2pt1’ Program
S4Vectors-0.20.1 S4 implementation of vector-like and list-like objects
SDMTools-1.1-221 Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercises
SKAT-1.3.2.1 SNP-Set (Sequence) Kernel Association Test
SNPRelate-1.16.0 Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
SPIA-2.34.0 Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
SQUAREM-2017.10-1 Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
SeqArray-1.22.6 Data Management of Large-scale Whole-genome Sequence Variant Calls
SeqVarTools-1.20.2 Tools for variant data
ShortRead-1.40.0 FASTQ input and manipulation
SimSeq-1.4.0 Nonparametric Simulation of RNA-Seq Data
SparseM-1.77 Sparse Linear Algebra
StanHeaders-2.18.1 C++ Header Files for Stan
SummarizedExperiment-1.12.0 SummarizedExperiment container
SuperLearner-2.0-24 Super Learner Prediction
SuppDists-1.1-9.4 Supplementary Distributions
TH.data-1.0-9 TH’s Data Archive
TMB-1.7.15 Template Model Builder: A General Random Effect Tool Inspired by
‘ADMB’
TTR-0.23-4 Technical Trading Rules
TeachingDemos-2.10 Demonstrations for Teaching and Learning
TitanCNA-1.20.1 Subclonal copy number and LOH prediction from whole genome sequencing of tumours
TraMineR-2.0-10 Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2 Annotation package for TxDb object(s)
UpSetR-1.3.3 A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
VGAM-1.0-6 Vector Generalized Linear and Additive Models
VIM-4.7.0 Visualization and Imputation of Missing Values
VariantAnnotation-1.28.13 Annotation of Genetic Variants
VennDiagram-1.6.20 Generate High-Resolution Venn and Euler Plots
WikidataR-1.4.0 API Client Library for ‘Wikidata’
WikipediR-1.5.0 A MediaWiki API Wrapper
WriteXLS-4.0.0 Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) Files
XML-3.98-1.16 Tools for Parsing and Generating XML Within R and S-Plus
XVector-0.22.0 Representation and manipulation of external sequences
abc-2.1 Tools for Approximate Bayesian Computation (ABC)
abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)
abind-1.4-5 Combine Multidimensional Arrays
acepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformations
adabag-4.2 Applies Multiclass AdaBoost.M1, SAMME and Bagging
ade4-1.7-13 Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
adegenet-2.1.1 Exploratory Analysis of Genetic and Genomic Data
adephylo-1.1-11 Exploratory Analyses for the Phylogenetic Comparative Method
affy-1.60.0 Methods for Affymetrix Oligonucleotide Arrays
affycoretools-1.54.0 Functions useful for those doing repetitive analyses with Affymetrix GeneChips
affyio-1.52.0 Tools for parsing Affymetrix data files
aggregation-1.0.1 p-Value Aggregation Methods
akima-0.6-2 Interpolation of Irregularly and Regularly Spaced Data
alr3-2.0.8 Data to Accompany Applied Linear Regression 3rd Edition
amap-0.8-16 Another Multidimensional Analysis Package
animation : 2.6 built in
annaffy-1.54.0 Annotation tools for Affymetrix biological metadata
annotate-1.60.1 Annotation for microarrays
aod-1.3 Analysis of Overdispersed Data
ape-5.2 Analyses of Phylogenetics and Evolution
argparser-0.4 Command-Line Argument Parser
arm-1.10-1 Data Analysis Using Regression and Multilevel/Hierarchical
Models
askpass-1.1 Safe Password Entry for R, Git, and SSH
asnipe-1.1.11 Animal Social Network Inference and Permutations for Ecologists
assertthat-0.2.0 Easy Pre and Post Assertions
audio-0.1-5.1 Audio Interface for R
aws.ec2metadata-0.1.5 Get EC2 Instance Metadata
aws.s3-0.3.12 ‘AWS S3’ Client Package
aws.signature-0.4.4 Amazon Web Services Request Signatures
backports-1.1.3 Reimplementations of Functions Introduced Since R-3.0.0
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
baySeq-2.16.0 Empirical Bayesian analysis of patterns of differential expression in count data
bayesm-3.1-1 Bayesian Inference for Marketing/Micro-Econometrics
bdsmatrix-1.3-3 Routines for Block Diagonal Symmetric Matrices
beanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)
beeswarm-0.2.3 The Bee Swarm Plot, an Alternative to Stripchart
benchmark-0.3-6 Benchmark Experiments Toolbox
bibtex-0.4.2 Bibtex Parser
biglm-0.9-1 bounded memory linear and generalized linear models
bigmemory-4.5.33 Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
bigmemory.sri-0.1.3 A shared resource interface for Bigmemory Project packages
bindr-0.1.1 Parametrized Active Bindings
bindrcpp-0.2.2 An ‘Rcpp’ Interface to Active Bindings
bio3d-2.3-4 Biological Structure Analysis
biom-0.3.12 An interface package (beta) for the BIOM file format.
biomaRt-2.38.0 Interface to BioMart databases (i.e. Ensembl)
biovizBase-1.30.1 Basic graphic utilities for visualization of genomic data.
bit-1.1-14 A Class for Vectors of 1-Bit Booleans
bit64-0.9-7 A S3 Class for Vectors of 64bit Integers
bitops-1.0-6 Bitwise Operations
blob-1.1.1 A Simple S3 Class for Representing Vectors of Binary Data
(‘BLOBS’)
bmp-0.3 Read Windows Bitmap (BMP) Images
bnlearn-4.4 Bayesian Network Structure Learning, Parameter Learning and
Inference
bold-0.8.6 Interface to Bold Systems API
boot-1.3-20 Bootstrap Functions (Originally by Angelo Canty for S)
bootstrap-2017.2 Functions for the Book “An Introduction to the Bootstrap”
breakaway-3.0 Species Richness Estimation and Modeling
brew-1.0-6 Templating Framework for Report Generation
brglm-0.6.1 Bias Reduction in Binomial-Response Generalized Linear Models
bridgedist-0.1.0 An Implementation of the Bridge Distribution with Logit-Link as
in Wang and Louis (2003)
bridgesampling-0.6-0 Bridge Sampling for Marginal Likelihoods and Bayes Factors
broom-0.5.1 Convert Statistical Analysis Objects into Tidy Tibbles
bst-0.3-15 Gradient Boosting
bumphunter-1.24.5 Bump Hunter
caTools-1.17.1.1 Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
calibrate-1.7.2 Calibration of Scatterplot and Biplot Axes
callr-3.1.1 Call R from R
car-3.0-2 Companion to Applied Regression
carData-3.0-2 Companion to Applied Regression Data Sets
caret-6.0-81 Classification and Regression Training
catdata-1.2.1 Categorical Data
cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
cgdsr-1.2.10 R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
cghFLasso-0.2-1 Detecting hot spot on CGH array data with fused lasso<U+000a>regression.
checkmate-1.8.5 Fast and Versatile Argument Checks
chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
chipseq-1.32.0 chipseq: A package for analyzing chipseq data
chron-2.3-53 Chronological Objects which can Handle Dates and Times
circlize-0.4.5 Circular Visualization
clValid-0.6-6 Validation of Clustering Results
class-7.3-14 Functions for Classification
classInt-0.3-1 Choose Univariate Class Intervals
cli-1.0.1 Helpers for Developing Command Line Interfaces
clipr-0.4.1 Read and Write from the System Clipboard
clisymbols-1.2.0 Unicode Symbols at the R Prompt
clue-0.3-57 Cluster Ensembles
cluster-2.0.7-1 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et
al.
clusterGeneration-1.3.4 Random Cluster Generation (with Specified Degree of Separation)
clusterRepro-0.9 Reproducibility of Gene Expression Clusters
clustree-0.2.2 Visualise Clusterings at Different Resolutions
coda-0.19-2 Output Analysis and Diagnostics for MCMC
codetools-0.2-16 Code Analysis Tools for R
coin-1.2-2 Conditional Inference Procedures in a Permutation Test Framework
colorspace-1.3-2 A Toolbox for Manipulating and Assessing Colors and Palettes
colourpicker-1.0 A Colour Picker Tool for Shiny and for Selecting Colours in
Plots
combinat-0.0-8 combinatorics utilities
commonmark-1.7 High Performance CommonMark and Github Markdown Rendering in R
compare-0.2-6 Comparing Objects for Differences
compositions-1.40-2 Compositional Data Analysis
config-0.3 Manage Environment Specific Configuration Values
copula-0.999-19 Multivariate Dependence with Copulas
corpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlation
cowplot-0.9.3 Streamlined Plot Theme and Plot Annotations for ‘ggplot2’
coxme-2.2-10 Mixed Effects Cox Models
crayon-1.3.4 Colored Terminal Output
crosstalk-1.0.0 Inter-Widget Interactivity for HTML Widgets
crul-0.6.0 HTTP Client
csSAM-1.2.4 csSAM - cell-specific Significance Analysis of Microarrays
cubature-2.0.3 Adaptive Multivariate Integration over Hypercubes
cummeRbund-2.24.0 Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
curl-3.2 A Modern and Flexible Web Client for R
cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
cytolib-1.4.1 C++ infrastructure for representing and interacting with the gated cytometry
d3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from R
data.table-1.11.8 Extension of data.frame
datasets built in
dbplyr-1.2.2 A ‘dplyr’ Back End for Databases
ddalpha-1.3.7 Depth-Based Classification and Calculation of Data Depth
deSolve-1.21 Solvers for Initial Value Problems of Differential Equations
(‘ODE’, ‘DAE’, ‘DDE’)
deal-1.2-39 Learning Bayesian Networks with Mixed Variables
debugme-1.1.0 Debug R Packages
degreenet-1.3-3 Models for Skewed Count Distributions Relevant to Networks
deldir-0.1-15 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
dendextend-1.9.0 Extending ‘dendrogram’ Functionality in R
derfinder-1.16.1 Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
derfinderHelper-1.16.1 derfinder helper package
desc-1.2.0 Manipulate DESCRIPTION Files
descr-1.1.4 Descriptive Statistics
devtools-2.0.1 Tools to Make Developing R Packages Easier
dfoptim-2018.2-1 Derivative-Free Optimization
diagram-1.6.4 Functions for Visualising Simple Graphs (Networks), Plotting
Flow Diagrams
diamonds-1.0-5 Analysis and sampling grids from diamond partitions
dichromat-2.0-0 Color Schemes for Dichromats
digest-0.6.18 Create Compact Hash Digests of R Objects
dimRed-0.2.2 A Framework for Dimensionality Reduction
diptest-0.75-7 Hartigan’s Dip Test Statistic for Unimodality - Corrected
dismo-1.1-4 Species Distribution Modeling
distillery-1.0-4 Method Functions for Confidence Intervals and to Distill
Information from an Object
distr-2.7.0 Object Oriented Implementation of Distributions
distrEx-2.7.0 Extensions of Package ‘distr’
diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis
Package
doMC-1.3.5 Foreach Parallel Adaptor for ‘parallel’
doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
doParallel-1.0.14 Foreach Parallel Adaptor for the ‘parallel’ Package
doRNG-1.7.1 Generic Reproducible Parallel Backend for ‘foreach’ Loops
doSNOW-1.0.16 Foreach Parallel Adaptor for the ‘snow’ Package
dotCall64-1.0-0 Enhanced Foreign Function Interface Supporting Long Vectors
downloader-0.4 Download Files over HTTP and HTTPS
dplyr-0.7.8 A Grammar of Data Manipulation
dtangle-0.3.1 Cell Type Deconvolution from Gene Expressions
dtw-1.20-1 Dynamic Time Warping Algorithms
dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
dynamicTreeCut-1.63-1 Methods for Detection of Clusters in Hierarchical Clustering
Dendrograms
e1071-1.7-0 Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
edgeR-3.24.3 Empirical Analysis of Digital Gene Expression Data in R
elasticnet-1.1.1 Elastic-Net for Sparse Estimation and Sparse PCA
ellipse-0.4.1 Functions for Drawing Ellipses and Ellipse-Like Confidence
Regions
ellipsis-0.1.0 Tools for Working with …
emulator-1.2-17 Bayesian Emulation of Computer Programs
energy-1.7-5 E-Statistics: Multivariate Inference via the Energy of Data
ensembldb-2.6.7 Utilities to create and use Ensembl-based annotation databases
ergm-3.9.4 Fit, Simulate and Diagnose Exponential-Family Models for
Networks
ergm.count-3.3.0 Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
evaluate-0.12 Parsing and Evaluation Tools that Provide More Details than the
Default
expm-0.999-3 Matrix Exponential, Log, ‘etc’
expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
extRemes-2.0-9 Extreme Value Analysis
extrafont-0.17 Tools for using fonts
extrafontdb-1.0 Package for holding the database for the extrafont package
fail-1.3 File Abstraction Interface Layer (FAIL)
fansi-0.4.0 ANSI Control Sequence Aware String Functions
farver-1.1.0 Vectorised Colour Conversion and Comparison
fastICA-1.2-1 FastICA Algorithms to Perform ICA and Projection Pursuit
fastcluster-1.1.25 Fast Hierarchical Clustering Routines for R and ‘Python’
fastmatch-1.1-0 Fast match() function
fastseg-1.28.0 fastseg - a fast segmentation algorithm
fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
fda-2.4.8 Functional Data Analysis
fdrtool-1.2.15 Estimation of (Local) False Discovery Rates and Higher Criticism
feather-0.3.1 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-1.0-4 Fast FFT and DCT Based on the FFTW Library
fftwtools-0.9-8 Wrapper for ‘FFTW3’ Includes: One-Dimensional Univariate,
One-Dimensional Multivariate, and Two-Dimensional Transform
fields-9.6 Tools for Spatial Data
filehash-2.4-1 Simple Key-Value Database
fishMod-0.29 Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta
Log-Normal Models
fit.models-0.5-14 Compare Fitted Models
fitdistrplus-1.0-11 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-2.3-14 Flexible Mixture Modeling
flowClust-3.20.1 Clustering for Flow Cytometry
flowCore-1.48.1 flowCore: Basic structures for flow cytometry data
flowStats-3.40.1 Statistical methods for the analysis of flow cytometry data
flowViz-1.46.1 Visualization for flow cytometry
flowWorkspace-3.30.2 Infrastructure for representing and interacting with gated and ungated cytometry data sets.
fma-2.3 Data Sets from “Forecasting: Methods and Applications” by
Makridakis, Wheelwright & Hyndman (1998)
forcats-0.3.0 Tools for Working with Categorical Variables (Factors)
foreach-1.4.4 Provides Foreach Looping Construct for R
forecast-8.4 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-1.5 Format R Code Automatically
fossil-0.3.7 Palaeoecological and Palaeogeographical Analysis Tools
fpc-2.1-11.1 Flexible Procedures for Clustering
fpp-0.5 Data for “Forecasting: principles and practice”
fracdiff-1.4-2 Fractionally differenced ARIMA aka ARFIMA(p,d,q) models
fs-1.2.6 Cross-Platform File System Operations Based on ‘libuv’
fts-0.9.9.2 R Interface to ‘tslib’ (a Time Series Library in C++)
futile.logger-1.4.3 A Logging Utility for R
futile.options-1.0.1 Futile Options Management
future-1.10.0 Unified Parallel and Distributed Processing in R for Everyone
gage-2.32.1 Generally Applicable Gene-set Enrichment for Pathway Analysis
gam-1.16 Generalized Additive Models
gamlss-5.1-2 Generalised Additive Models for Location Scale and Shape
gamlss.data-5.1-0 GAMLSS Data
gamlss.dist-5.1-1 Distributions for Generalized Additive Models for Location Scale
and Shape
gamlss.tr-5.1-0 Generating and Fitting Truncated `gamlss.family’ Distributions
gamm4-0.2-5 Generalized Additive Mixed Models using ‘mgcv’ and ‘lme4’
gap-1.1-22 Genetic Analysis Package
gapfill-0.9.6 Fill Missing Values in Satellite Data
gbRd-0.4-11 Utilities for processing Rd objects and files
gbm-2.1.4 Generalized Boosted Regression Models
gclus-1.3.1 Clustering Graphics
gcrma-2.54.0 Background Adjustment Using Sequence Information
gdalUtils-2.0.1.14 Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities
gdata-2.18.0 Various R Programming Tools for Data Manipulation
gdistance-1.2-2 Distances and Routes on Geographical Grids
gdsfmt-1.18.1 R Interface to CoreArray Genomic Data Structure (GDS) files
gee-4.13-19 Generalized Estimation Equation Solver
geepack-1.2-1 Generalized Estimating Equation Package
geiger-2.0.6 Analysis of Evolutionary Diversification
geneLenDataBase-1.18.0 Lengths of mRNA transcripts for a number of genomes
genefilter-1.64.0 genefilter: methods for filtering genes from high-throughput experiments
geneplotter-1.60.0 Graphics related functions for Bioconductor
generics-0.0.2 Common S3 Generics not Provided by Base R Methods Related to
Model Fitting
genoset-1.38.0 A RangedSummarizedExperiment with methods for copy number analysis
geometry-0.3-6 Mesh Generation and Surface Tessellation
getopt-1.20.2 C-Like ‘getopt’ Behavior
ggExtra-0.8 Add Marginal Histograms to ‘ggplot2’, and More ‘ggplot2’
Enhancements
ggbeeswarm-0.6.0 Categorical Scatter (Violin Point) Plots
ggbio-1.30.0 Visualization tools for genomic data
ggforce-0.1.3 Accelerating ‘ggplot2’
ggm-2.3 Functions for graphical Markov models
ggplot2-3.1.0 Create Elegant Data Visualisations Using the Grammar of Graphics
ggraph-1.0.2 An Implementation of Grammar of Graphics for Graphs and Networks
ggrepel-0.8.0 Automatically Position Non-Overlapping Text Labels with
‘ggplot2’
ggridges-0.5.1 Ridgeline Plots in ‘ggplot2’
ggthemes-4.1.0 Extra Themes, Scales and Geoms for ‘ggplot2’
ggtree-1.14.6 an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
ggvis-0.4.4 Interactive Grammar of Graphics
gh-1.0.1 ‘GitHub’ ‘API’
git2r-0.23.0 Provides Access to Git Repositories
glasso-1.10 Graphical Lasso: Estimation of Gaussian Graphical Models
gllvm-1.1.0 Generalized Linear Latent Variable Models
glmmML-1.0.3 Generalized Linear Models with Clustering
glmmTMB-0.2.2.0 Generalized Linear Mixed Models using Template Model Builder
glmnet-2.0-16 Lasso and Elastic-Net Regularized Generalized Linear Models
glmpath-0.98 L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Model
globals-0.12.4 Identify Global Objects in R Expressions
glue-1.3.0 Interpreted String Literals
gmm-1.6-2 Generalized Method of Moments and Generalized Empirical
Likelihood
gmodels-2.18.1 Various R Programming Tools for Model Fitting
goftest-1.1-1 Classical Goodness-of-Fit Tests for Univariate Distributions
gomms-1.0 GLM-Based Ordination Method
goseq-1.34.1 Gene Ontology analyser for RNA-seq and other length biased data
gower-0.1.2 Gower’s Distance
gplots-3.0.1 Various R Programming Tools for Plotting Data
grDevices built in
graph-1.60.0 graph: A package to handle graph data structures
graphics built in
grid built in
gridBase-0.4-7 Integration of base and grid graphics
gridExtra-2.3 Miscellaneous Functions for “Grid” Graphics
grpreg-3.2-0 Regularization Paths for Regression Models with Grouped
Covariates
gsalib-2.1 Utility Functions For GATK
gsl-1.9-10.3 Wrapper for the Gnu Scientific Library
gsubfn-0.7 Utilities for Strings and Function Arguments
gsw-1.0-5 Gibbs Sea Water Functions
gtable-0.2.0 Arrange ‘Grobs’ in Tables
gtools-3.8.1 Various R Programming Tools
h2o-3.22.1.1 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-2.0.0 Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files
hdf5r-1.0.1 Interface to the ‘HDF5’ Binary Data Format
heatmap3-1.1.1 An Improved Heatmap Package
hexbin-1.27.2 Hexagonal Binning Routines
hgu133plus2.db-3.2.3 Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2)
highr-0.7 Syntax Highlighting for R Source Code
hms-0.4.2 Pretty Time of Day
hopach-2.42.0 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
htmlTable-1.12 Advanced Tables for Markdown/HTML
htmltools-0.3.6 Tools for HTML
htmlwidgets-1.3 HTML Widgets for R
httpcode-0.2.0 ‘HTTP’ Status Code Helper
httpuv-1.4.5.1 HTTP and WebSocket Server Library
httr-1.4.0 Tools for Working with URLs and HTTP
huge-1.2.7 High-Dimensional Undirected Graph Estimation
hwriter-1.3.2 HTML Writer - Outputs R objects in HTML format
ica-1.0-2 Independent Component Analysis
idr-1.2 Irreproducible discovery rate
igraph-1.2.2 Network Analysis and Visualization
igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
illuminaio-0.24.0 Parsing Illumina Microarray Output Files
imager-0.41.1 Image Processing Library Based on ‘CImg’
impute-1.56.0 impute: Imputation for microarray data
ineq-0.2-13 Measuring Inequality, Concentration, and Poverty
inferference-1.0.0 Methods for Causal Inference with Interference
influenceR-0.1.0 Software Tools to Quantify Structural Importance of Nodes in a
Network
infotheo-1.2.0 Information-Theoretic Measures
ini-0.3.1 Read and Write ‘.ini’ Files
inline-0.3.15 Functions to Inline C, C++, Fortran Function Calls from R
interactiveDisplayBase-1.20.0 Base package for enabling powerful shiny web displays of Bioconductor objects
interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
inum-1.0-0 Interval and Enum-Type Representation of Vectors
ipred-0.9-8 Improved Predictors
irace-3.1 Iterated Racing for Automatic Algorithm Configuration
irlba-2.3.2 Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
iterators-1.0.10 Provides Iterator Construct for R
itertools-0.1-3 Iterator Tools
its-1.1.8 Irregular Time Series
jomo-2.6-5 Multilevel Joint Modelling Multiple Imputation
jpeg-0.1-8 Read and write JPEG images
jsonlite-1.6 A Robust, High Performance JSON Parser and Generator for R
kernlab-0.9-27 Kernel-Based Machine Learning Lab
kin.cohort-0.7 Analysis of Kin-Cohort Studies
kinship2-1.6.4 Pedigree Functions
klaR-0.6-14 Classification and Visualization
knitr-1.21 A General-Purpose Package for Dynamic Report Generation in R
kohonen-3.0.8 Supervised and Unsupervised Self-Organising Maps
ks-1.11.3 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-2.0.1 Manipulating Labelled Data
laeken-0.4.6 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-0.7.5 Utilities for Delaying Function Execution
lattice-0.20-38 Trellis Graphics for R
latticeExtra-0.6-28 Extra Graphical Utilities Based on Lattice
lava-1.6.4 Latent Variable Models
lavaan-0.6-3 Latent Variable Analysis
lazy-1.2-16 Lazy Learning for Local Regression
lazyeval-0.2.1 Lazy (Non-Standard) Evaluation
leaps-3.0 Regression Subset Selection
lhs-0.16 Latin Hypercube Samples
libcoin-1.0-2 Linear Test Statistics for Permutation Inference
limSolve-1.5.5.3 Solving Linear Inverse Models
limma-3.38.3 Linear Models for Microarray Data
lintr-1.0.3 A ‘Linter’ for R Code
liquidSVM-1.2.2 A Fast and Versatile SVM Package
listenv-0.7.0 Environments Behaving (Almost) as Lists
lme4-1.1-19 Linear Mixed-Effects Models using ‘Eigen’ and S4
lmtest-0.9-36 Testing Linear Regression Models
locfdr-1.1-8 Computes Local False Discovery Rates
locfit-1.5-9.1 Local Regression, Likelihood and Density Estimation.
logcondens-2.1.5 Estimate a Log-Concave Probability Density from Iid Observations
logistf-1.23 Firth’s Bias-Reduced Logistic Regression
logspline-2.1.11 Routines for Logspline Density Estimation
lokern-1.1-8 Kernel Regression Smoothing with Local or Global Plug-in
Bandwidth
longitudinal-1.1.12 Analysis of Multiple Time Course Data
longmemo-1.1-1 Statistics for Long-Memory Processes (Book Jan Beran), and
Related Functionality
lpSolve-5.6.13 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
lpridge-1.0-8 Local Polynomial (Ridge) Regression
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-2.34.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
maSigPro-1.54.0 Significant Gene Expression Profile Differences in Time Course Gene Expression Data
magic-1.5-9 Create and Investigate Magic Squares
magick-2.0 Advanced Graphics and Image-Processing in R
magrittr-1.5 A Forward-Pipe Operator for R
manipulateWidget-0.10.0 Add Even More Interactivity to Interactive Charts
mapdata-2.3.0 Extra Map Databases
mapproj-1.2.6 Map Projections
maps-3.3.0 Draw Geographical Maps
maptools-0.9-4 Tools for Handling Spatial Objects
markdown-0.9 Render Markdown with the C Library ‘Sundown’
marray-1.60.0 Exploratory analysis for two-color spotted microarray data
matrixStats-0.54.0 Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
matrixcalc-1.0-3 Collection of functions for matrix calculations
maxLik-1.3-4 Maximum Likelihood Estimation and Related Tools
mboost-2.9-1 Model-Based Boosting
mclust-5.4.2 Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
mcmc-0.9-5 Markov Chain Monte Carlo
mediation-4.4.6 Causal Mediation Analysis
memoise-1.1.0 Memoisation of Functions
memuse-4.0-0 Memory Estimation Utilities
metagenomeSeq-1.24.1 Statistical analysis for sparse high-throughput sequencing
metap-1.0 Meta-Analysis of Significance Values
methods built in
methylumi-2.28.0 Handle Illumina methylation data
mgcv-1.8-26 Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
mi-1.0 Missing Data Imputation and Model Checking
mice-3.4.0 Multivariate Imputation by Chained Equations
mime-0.6 Map Filenames to MIME Types
minfi-1.28.4 Analyze Illumina Infinium DNA methylation arrays
miniUI-0.1.1.1 Shiny UI Widgets for Small Screens
minpack.lm-1.2-1 R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
minqa-1.2.4 Derivative-free optimization algorithms by quadratic<U+000a>approximation
misc3d-0.8-4 Miscellaneous 3D Plots
miscTools-0.6-22 Miscellaneous Tools and Utilities
missForest-1.4 Nonparametric Missing Value Imputation using Random Forest
mitml-0.3-6 Tools for Multiple Imputation in Multilevel Modeling
mixOmics-6.6.2 Omics Data Integration Project
mixtools-1.1.0 Tools for Analyzing Finite Mixture Models
mlbench-2.1-1 Machine Learning Benchmark Problems
mlegp-3.1.7 Maximum Likelihood Estimates of Gaussian Processes
mlogit-0.3-0 Multinomial Logit Models
mlr-2.13 Machine Learning in R
mltools-0.3.5 Machine Learning Tools
mnormt-1.5-5 The Multivariate Normal and t Distributions
modelr-0.1.2 Modelling Functions that Work with the Pipe
modeltools-0.2-22 Tools and Classes for Statistical Models
moments-0.14 Moments, cumulants, skewness, kurtosis and related tests
mondate-0.10.01.02 Keep track of dates in terms of months
mpath-0.3-5 Regularized Linear Models
msm-1.6.6 Multi-State Markov and Hidden Markov Models in Continuous Time
multcomp-1.4-8 Simultaneous Inference in General Parametric Models
multicool-0.1-10 Permutations of Multisets in Cool-Lex Order
multtest-2.38.0 Resampling-based multiple hypothesis testing
munsell-0.5.0 Utilities for Using Munsell Colours
mvabund-3.13.1 Statistical Methods for Analysing Multivariate Abundance Data
mvtnorm-1.0-8 Multivariate Normal and t Distributions
natserv-0.1.4 ‘NatureServe’ Interface
ncbit-2013.03.29 retrieve and build NBCI taxonomic data
ncdf4-1.16.1 Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
ncdfFlow-2.28.1 ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
network-1.13.0.1 Classes for Relational Data
networkDynamic-0.9.0 Dynamic Extensions for Network Objects
networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Sampling
neuRosim-0.2-12 Functions to Generate fMRI Data Including Activated Data, Noise
Data and Resting State Data
nleqslv-3.3.2 Solve Systems of Nonlinear Equations
nlme-3.1-137 Linear and Nonlinear Mixed Effects Models
nloptr-1.2.1 R Interface to NLopt
nnet-7.3-12 Feed-Forward Neural Networks and Multinomial Log-Linear Models
nnls-1.4 The Lawson-Hanson algorithm for non-negative least squares<U+000a>(NNLS)
nor1mix-1.2-3 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and
Methods)
np-0.60-9 Nonparametric Kernel Smoothing Methods for Mixed Data Types
npsurv-0.4-0 Nonparametric Survival Analysis
numDeriv-2016.8-1 Accurate Numerical Derivatives
nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
oce-1.0-1 Analysis of Oceanographic Data
oddsratio-1.0.3 Odds Ratio Calculation for GAM(M)s & GLM(M)s
oligoClasses-1.44.0 Classes for high-throughput arrays supported by oligo and crlmm
openCyto-1.20.2 Hierarchical Gating Pipeline for flow cytometry data
openssl-1.1 Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
openxlsx-4.1.0 Read, Write and Edit XLSX Files
optmatch-0.9-10 Functions for Optimal Matching
optparse-1.6.0 Command Line Option Parser
ordinal-2018.8-25 Regression Models for Ordinal Data
org.Hs.eg.db-3.7.0 Genome wide annotation for Human
pROC-1.13.0 Display and Analyze ROC Curves
packrat-0.5.0 A Dependency Management System for Projects and their R Package
Dependencies
pan-1.6 Multiple Imputation for Multivariate Panel or Clustered Data
parallelMap-1.3 Unified Interface to Parallelization Back-Ends
parsedate-1.1.3 Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formats
partools-1.1.6 Tools for the ‘Parallel’ Package
party-1.3-1 A Laboratory for Recursive Partytioning
partykit-1.2-2 A Toolkit for Recursive Partytioning
pastecs-1.3.21 Package for Analysis of Space-Time Ecological Series
pbapply-1.3-4 Adding Progress Bar to ‘*apply’ Functions
pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
pbkrtest-0.4-7 Parametric Bootstrap and Kenward Roger Based Methods for Mixed
Model Comparison
pbs-1.1 Periodic B Splines
pcaMethods-1.74.0 A collection of PCA methods
pcaPP-1.9-73 Robust PCA by Projection Pursuit
pdist-1.2 Partitioned Distance Function
pedigree-1.4 Pedigree functions
pedigreemm-0.3-3 Pedigree-based mixed-effects models
penalized-0.9-51 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
peperr-1.1-7 Parallelised Estimation of Prediction Error
perm-1.0-0.0 Exact or Asymptotic permutation tests
permute-0.9-4 Functions for Generating Restricted Permutations of Data
phangorn-2.4.0 Phylogenetic Reconstruction and Analysis
pheatmap-1.0.10 Pretty Heatmaps
phylobase-0.8.4 Base Package for Phylogenetic Structures and Comparative Data
pillar-1.3.1 Coloured Formatting for Columns
pim-2.0.1 Fit Probabilistic Index Models
pinfsc50-1.1.0 Sequence (‘FASTA’), Annotation (‘GFF’) and Variants (‘VCF’) for
17 Samples of ‘P. Infestans” and 1 ‘P. Mirabilis’
pixmap-0.4-11 Bitmap Images (``Pixel Maps’’)
pkgbuild-1.0.2 Find Tools Needed to Build R Packages
pkgconfig-2.0.2 Private Configuration for ‘R’ Packages
pkgload-1.0.2 Simulate Package Installation and Attach
pkgmaker-0.27 Development Utilities for R Packages
plogr-0.2.0 The ‘plog’ C++ Logging Library
plot3D-1.1.1 Plotting Multi-Dimensional Data
plot3Drgl-1.0.1 Plotting Multi-Dimensional Data - Using ‘rgl’
plotly-4.8.0 Create Interactive Web Graphics via ‘plotly.js’
plotrix-3.7-4 Various Plotting Functions
pls-2.7-0 Partial Least Squares and Principal Component Regression
plyr-1.8.4 Tools for Splitting, Applying and Combining Data
png-0.1-7 Read and write PNG images
polspline-1.1.13 Polynomial Spline Routines
polyclip-1.9-1 Polygon Clipping
polyester-1.18.0 Simulate RNA-seq reads
polynom-1.3-9 A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulations
prabclus-2.2-6 Functions for Clustering and Testing of Presence-Absence,
Abundance and Multilocus Genetic Data
pracma-2.2.2 Practical Numerical Math Functions
praise-1.0.0 Praise Users
preprocessCore-1.44.0 A collection of pre-processing functions
prettyunits-1.0.2 Pretty, Human Readable Formatting of Quantities
processx-3.2.1 Execute and Control System Processes
prodlim-2018.04.18 Product-Limit Estimation for Censored Event History Analysis
profileModel-0.5-9 Profiling Inference Functions for Various Model Classes
progress-1.2.0 Terminal Progress Bars
promises-1.0.1 Abstractions for Promise-Based Asynchronous Programming
proto-1.0.0 Prototype Object-Based Programming
proxy-0.4-22 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-1.8.10 Procedures for Psychological, Psychometric, and Personality
Research
psychotools-0.5-0 Psychometric Modeling Infrastructure
pulsar-0.3.4 Parallel Utilities for Lambda Selection along a Regularization
Path
purrr-0.2.5 Functional Programming Tools
pvclust-2.0-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
qgraph-1.5 Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
qpdf-1.1 Split, Combine and Compress PDF Files
qrnn-2.0.3 Quantile Regression Neural Network
qtl-1.44-9 Tools for Analyzing QTL Experiments
quadprog-1.5-5 Functions to Solve Quadratic Programming Problems
quantmod-0.4-13 Quantitative Financial Modelling Framework
quantreg-5.38 Quantile Regression
quantsmooth-1.48.0 Quantile smoothing and genomic visualization of array data
questionr-0.7.0 Functions to Make Surveys Processing Easier
qvalue-2.14.1 Q-value estimation for false discovery rate control
qvcalc-0.9-1 Quasi Variances for Factor Effects in Statistical Models
r2d3-0.2.3 Interface to ‘D3’ Visualizations
rARPACK-0.11-0 Solvers for Large Scale Eigenvalue and SVD Problems
rGADEM-2.30.0 de novo motif discovery
rJava-0.9-10 Low-Level R to Java Interface
randomForest-4.6-14 Breiman and Cutler’s Random Forests for Classification and
Regression
randomForestSRC-2.7.0 Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
ranger-0.10.1 A Fast Implementation of Random Forests
rappdirs-0.3.1 Application Directories: Determine Where to Save Data, Caches,
and Logs
raster-2.8-4 Geographic Data Analysis and Modeling
rbenchmark-1.0.0 Benchmarking routine for R
rcmdcheck-1.3.2 Run ‘R CMD check’ from ‘R’ and Capture Results
readbitmap-0.1.5 Simple Unified Interface to Read Bitmap Images
(BMP,JPEG,PNG,TIFF)
readr-1.3.1 Read Rectangular Text Data
readxl-1.2.0 Read Excel Files
recipes-0.1.4 Preprocessing Tools to Create Design Matrices
refund-0.1-17 Regression with Functional Data
registry-0.5 Infrastructure for R Package Registries
regress-1.3-15 Gaussian Linear Models with Linear Covariance Structure
regtools-1.0.1 Regression Tools
relations-0.6-8 Data Structures and Algorithms for Relations
relevent-1.0-4 Relational Event Models
rematch-1.0.1 Match Regular Expressions with a Nicer ‘API’
remotes-2.0.2 R Package Installation from Remote Repositories, Including
‘GitHub’
rentrez-1.2.1 ‘Entrez’ in R
repr-0.19.2 Serializable Representations
reprex-0.2.1 Prepare Reproducible Example Code via the Clipboard
reshape-0.8.8 Flexibly Reshape Data
reshape2-1.4.3 Flexibly Reshape Data: A Reboot of the Reshape Package
reticulate-1.10 Interface to ‘Python’
rex-1.1.2 Friendly Regular Expressions
rgdal-1.3-6 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-0.99.16 3D Visualization Using OpenGL
rhdf5-2.26.2 HDF5 interface to R
rio-0.5.16 A Swiss-Army Knife for Data I/O
ritis-0.7.6 Integrated Taxonomic Information System Client
rjags-4-8 Bayesian Graphical Models using MCMC
rjson-0.2.20 JSON for R
rlang-0.3.2 Functions for Base Types and Core R and ‘Tidyverse’ Features
rlecuyer-0.3-4 R Interface to RNG with Multiple Streams
rmarkdown-1.11 Dynamic Documents for R
rmeta-3.0 Meta-Analysis
rms-5.1-2 Regression Modeling Strategies
rncl-0.8.3 An Interface to the Nexus Class Library
rngtools-1.3.1 Utility Functions for Working with Random Number Generators
robustbase-0.93-3 Basic Robust Statistics
rootSolve-1.7 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
rotl-3.0.5 Interface to the ‘Open Tree of Life’ API
roxygen2-6.1.1 In-Line Documentation for R
rpart-4.1-13 Recursive Partitioning and Regression Trees
rprojroot-1.3-2 Finding Files in Project Subdirectories
rrcov-1.4-7 Scalable Robust Estimators with High Breakdown Point
rredlist-0.5.0 ‘IUCN’ Red List Client
rsconnect-0.8.13 Deployment Interface for R Markdown Documents and Shiny
Applications
rslurm-0.4.0 Submit R Calculations to a Slurm Cluster
rstudioapi-0.8 Safely Access the RStudio API
rtracklayer-1.42.2 R interface to genome annotation files and the UCSC genome browser
rvcheck-0.1.3 R/Package Version Check
rversions-1.0.3 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
rvest-0.3.2 Easily Harvest (Scrape) Web Pages
rzmq-0.9.6 R Bindings for ‘ZeroMQ’
samr-3.0 SAM: Significance Analysis of Microarrays
sandwich-2.5-0 Robust Covariance Matrix Estimators
scales-1.0.0 Scale Functions for Visualization
scatterplot3d-0.3-41 3D Scatter Plot
scidb-2.0.0 An R Interface to SciDB
seewave-2.1.0 Sound Analysis and Synthesis
segmented-0.5-3.0 Regression Models with Break-Points / Change-Points Estimation
selectr-0.4-1 Translate CSS Selectors to XPath Expressions
sem-3.1-9 Structural Equation Models
sendmailR-1.2-1 send email using R
seqLogo-1.48.0 Sequence logos for DNA sequence alignments
seqinr-3.4-5 Biological Sequences Retrieval and Analysis
sessioninfo-1.1.1 R Session Information
sets-1.0-18 Sets, Generalized Sets, Customizable Sets and Intervals
sf-0.7-2 Simple Features for R
sfsmisc-1.1-3 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
shape-1.4.4 Functions for Plotting Graphical Shapes, Colors
shapefiles-0.7 Read and Write ESRI Shapefiles
shiny-1.2.0 Web Application Framework for R
shinyBS-0.61 Twitter Bootstrap Components for Shiny
shinyFiles-0.7.2 A Server-Side File System Viewer for Shiny
shinycssloaders-0.2.0 Add CSS Loading Animations to ‘shiny’ Outputs
shinydashboard-0.7.1 Create Dashboards with ‘Shiny’
shinyjs-1.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
shinythemes-1.1.2 Themes for Shiny
sigaR-1.30.0 Statistics for Integrative Genomics Analyses in R
siggenes-1.56.0 Multiple testing using SAM and Efron’s empirical Bayes approaches
signal-0.7-6 Signal Processing
slam-0.1-44 Sparse Lightweight Arrays and Matrices
sm-2.2-5.6 Smoothing Methods for Nonparametric Regression and Density
Estimation
smoother-1.1 Functions Relating to the Smoothing of Numerical Data
sn-1.5-3 The Skew-Normal and Related Distributions Such as the Skew-t
sna-2.4 Tools for Social Network Analysis
snow-0.4-3 Simple Network of Workstations
snowfall-1.84-6.1 Easier cluster computing (based on snow).
snpStats-1.32.0 SnpMatrix and XSnpMatrix classes and methods
solrium-1.0.2 General Purpose R Interface to ‘Solr’
som-0.3-5.1 Self-Organizing Map
soundecology-1.3.3 Soundscape Ecology
sourcetools-0.1.7 Tools for Reading, Tokenizing and Parsing R Code
sp-1.3-1 Classes and Methods for Spatial Data
spData-0.2.9.6 Datasets for Spatial Analysis
spam-2.2-1 SPArse Matrix
sparklyr-1.0.0 R Interface to Apache Spark
spatial-7.3-11 Functions for Kriging and Point Pattern Analysis
spatstat-1.57-1 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-0.8-1 Spatial Dependence: Weighting Schemes, Statistics and Models
splines built in
sqldf-0.4-11 Manipulate R Data Frames Using SQL
ssgraph-1.7 Bayesian Graphical Estimation using Spike-and-Slab Priors
stabledist-0.7-1 Stable Distribution Functions
stabs-0.6-3 Stability Selection with Error Control
startupmsg-0.9.5 Utilities for Start-Up Messages
statmod-1.4.30 Statistical Modeling
statnet-2018.10 Software Tools for the Statistical Analysis of Network Data
statnet.common-4.1.4 Common R Scripts and Utilities Used by the Statnet Project
Software
stats built in
stats4 built in
stringdist-0.9.5.1 Approximate String Matching and String Distance Functions
stringi-1.2.4 Character String Processing Facilities
stringr-1.3.1 Simple, Consistent Wrappers for Common String Operations
strucchange-1.5-1 Testing, Monitoring, and Dating Structural Changes
subplex-1.5-4 Unconstrained Optimization using the Subplex Algorithm
survey-3.35-1 Analysis of Complex Survey Samples
survival-2.43-3 Survival Analysis
survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
svd-0.4.1 Interfaces to Various State-of-Art SVD and Eigensolvers
synapseClient 1.14-3
sys-3.1 Powerful and Reliable Tools for Running System Commands in R
systemPipeR-1.16.1 systemPipeR: NGS workflow and report generation environment
tables-0.8.7 Formula-Driven Table Generation
taxize-0.9.4 Taxonomic Information from Around the Web
tclust-1.4-1 Robust Trimmed Clustering
tensor-1.5 Tensor product of arrays
tensorA-0.36.1 Advanced Tensor Arithmetic with Named Indices
tergm-3.5.2 Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
testthat-2.0.1 Unit Testing for R
tibble-1.4.2 Simple Data Frames
tidygraph-1.1.1 A Tidy API for Graph Manipulation
tidyr-0.8.2 Easily Tidy Data with ‘spread()’ and ‘gather()’ Functions
tidyselect-0.2.5 Select from a Set of Strings
tidytree-0.2.4 A Tidy Tool for Phylogenetic Tree Data Manipulation
tidyverse-1.2.1 Easily Install and Load the ‘Tidyverse’
tiff-0.1-5 Read and write TIFF images
tilingArray-1.60.0 Transcript mapping with high-density oligonucleotide tiling arrays
timeDate-3043.102 Rmetrics - Chronological and Calendar Objects
timeSeries-3042.102 Rmetrics - Financial Time Series Objects
timereg-1.9.2 Flexible Regression Models for Survival Data
tinytex-0.9 Helper Functions to Install and Maintain ‘TeX Live’, and Compile
‘LaTeX’ Documents
tkWidgets-1.60.0 R based tk widgets
tkrplot-0.0-24 TK Rplot
tm-0.7-6 Text Mining Package
tmle-1.3.0-2 Targeted Maximum Likelihood Estimation
tmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distribution
tools built in
tree-1.0-39 Classification and Regression Trees
treeio-1.6.2 Base Classes and Functions for Phylogenetic Tree Input and Output
triebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’
trimcluster-0.1-2.1 Cluster Analysis with Trimming
tripack-1.3-8 Triangulation of Irregularly Spaced Data
trust-0.1-7 Trust Region Optimization
tseries-0.10-46 Time Series Analysis and Computational Finance
tseriesChaos-0.1-13 Analysis of Nonlinear Time Series
tsna-0.2.0 Tools for Temporal Social Network Analysis
tsne-0.1-3 T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
tuneR-1.3.3 Analysis of Music and Speech
tweedie-2.3.2 Evaluation of Tweedie Exponential Family Models
tweenr-1.0.1 Interpolate Data for Smooth Animations
ucminf-1.1-4 General-Purpose Unconstrained Non-Linear Optimization
udunits2-0.13 Udunits-2 Bindings for R
unbalanced-2.0 Racing for Unbalanced Methods Selection
uniqueAtomMat-0.1-3-2 Finding Unique or Duplicated Rows or Columns for Atomic Matrices
units-0.6-2 Measurement Units for R Vectors
urca-1.3-0 Unit Root and Cointegration Tests for Time Series Data
urltools-1.7.1 Vectorised Tools for URL Handling and Parsing
uroot-2.0-9 Unit Root Tests for Seasonal Time Series
usethis-1.4.0 Automate Package and Project Setup
utf8-1.1.4 Unicode Text Processing
utils built in
uuid-0.1-2 Tools for generating and handling of UUIDs
vcd-1.4-4 Visualizing Categorical Data
vcfR-1.8.0 Manipulate and Visualize VCF Data
vegan-2.5-3 Community Ecology Package
venn-1.7 Draw Venn Diagrams
vioplot-0.2 Violin Plot
vipor-0.4.5 Plot Categorical Data Using Quasirandom Noise and Density
Estimates
viridis-0.5.1 Default Color Maps from ‘matplotlib’
viridisLite-0.3.0 Default Color Maps from ‘matplotlib’ (Lite Version)
visNetwork-2.0.5 Network Visualization using ‘vis.js’ Library
vsn-3.50.0 Variance stabilization and calibration for microarray data
waveslim-1.7.5 Basic Wavelet Routines for One-, Two- And Three-Dimensional
Signal Processing
wavethresh-4.6.8 Wavelets Statistics and Transforms
webp-1.0 A New Format for Lossless and Lossy Image Compression
webshot-0.5.1 Take Screenshots of Web Pages
whisker-0.3-2 for R, logicless templating
widgetTools-1.60.0 Creates an interactive tcltk widget
wikitaxa-0.3.0 Taxonomic Information from ‘Wikipedia’
withr-2.1.2 Run Code ‘With’ Temporarily Modified Global State
worrms-0.3.0 World Register of Marine Species (WoRMS) Client
xfun-0.4 Miscellaneous Functions by ‘Yihui Xie’
xlsx-0.6.1 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
xlsxjars-0.6.1 Package required POI jars for the xlsx package
xml2-1.2.0 Parse XML
xopen-1.0.0 Open System Files, ‘URLs’, Anything
xtable-1.8-3 Export Tables to LaTeX or HTML
xts-0.11-2 eXtensible Time Series
yaml-2.2.0 Methods to Convert R Data to YAML and Back
zip-1.0.0 Cross-Platform ‘zip’ Compression
zlibbioc-1.28.0 An R packaged zlib-1.2.5
zoo-1.8-4 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)
Edit this Page via GitHub
Comment by Filing an Issue
Have Questions? Ask them here.