R packages available
Packages in library ‘/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/IRkernel/1.1.1-gimkl-2020a-R-4.0.1’:
git2r Provides Access to Git Repositories
IRdisplay 'Jupyter' Display Machinery
IRkernel Native R Kernel for the 'Jupyter Notebook'
pbdZMQ Programming with Big Data -- Interface to
'ZeroMQ'
repr Serializable Representations
uuid Tools for Generating and Handling of UUIDs
Packages in library ‘/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/R-bundle-Bioconductor/3.11-gimkl-2020a-R-4.0.1’:
ade4 Analysis of Ecological Data: Exploratory and
Euclidean Methods in Environmental Sciences
adegenet Exploratory Analysis of Genetic and Genomic
Data
admisc Adrian Dusa's Miscellaneous
affxparser Affymetrix File Parsing SDK
affy Methods for Affymetrix Oligonucleotide Arrays
affycoretools Functions useful for those doing repetitive
analyses with Affymetrix GeneChips
affyio Tools for parsing Affymetrix data files
AgiMicroRna Processing and Differential Expression Analysis
of Agilent microRNA chips
ALDEx2 Analysis Of Differential Abundance Taking
Sample Variation Into Account
ALL A data package
annaffy Annotation tools for Affymetrix biological
metadata
annotate Annotation for microarrays
AnnotationDbi Manipulation of SQLite-based annotations in
Bioconductor
AnnotationFilter Facilities for Filtering Bioconductor
Annotation Resources
AnnotationForge Tools for building SQLite-based annotation data
packages
AnnotationHub Client to access AnnotationHub resources
ballgown Flexible, isoform-level differential expression
analysis
batchelor Single-Cell Batch Correction Methods
baySeq Empirical Bayesian analysis of patterns of
differential expression in count data
beachmat Compiling Bioconductor to Handle Each Matrix
Type
beeswarm The Bee Swarm Plot, an Alternative to
Stripchart
bigassertr Assertion and Message Functions
bigparallelr Easy Parallel Tools
bigutilsr Utility Functions for Large-scale Data
Biobase Biobase: Base functions for Bioconductor
BiocFileCache Manage Files Across Sessions
BiocGenerics S4 generic functions used in Bioconductor
BiocManager Access the Bioconductor Project Package
Repository
BiocNeighbors Nearest Neighbor Detection for Bioconductor
Packages
BiocParallel Bioconductor facilities for parallel evaluation
BiocSingular Singular Value Decomposition for Bioconductor
Packages
BiocVersion Set the appropriate version of Bioconductor
packages
biomaRt Interface to BioMart databases (i.e. Ensembl)
biomformat An interface package for the BIOM file format
Biostrings Efficient manipulation of biological strings
biovizBase Basic graphic utilities for visualization of
genomic data.
blme Bayesian Linear Mixed-Effects Models
BSgenome Software infrastructure for efficient
representation of full genomes and their SNPs
BSgenome.Cfamiliaris.UCSC.canFam3
Full genome sequences for Canis lupus
familiaris (UCSC version canFam3)
BSgenome.Hsapiens.UCSC.hg19
Full genome sequences for Homo sapiens (UCSC
version hg19, based on GRCh37.p13)
BSgenome.Hsapiens.UCSC.hg38
Full genome sequences for Homo sapiens (UCSC
version hg38, based on GRCh38.p12)
BSgenome.Mmusculus.UCSC.mm10
Full genome sequences for Mus musculus (UCSC
version mm10)
bumphunter Bump Hunter
Category Category Analysis
ccdata Data for Combination Connectivity Mapping
(ccmap) Package
CGHbase CGHbase: Base functions and classes for
arrayCGH data analysis.
colorRamps Builds color tables
combinat combinatorics utilities
ConsensusClusterPlus ConsensusClusterPlus
conumee Enhanced copy-number variation analysis using
Illumina DNA methylation arrays
cummeRbund Analysis, exploration, manipulation, and
visualization of Cufflinks high-throughput
sequencing data.
cytolib C++ infrastructure for representing and
interacting with the gated cytometry
dada2 Accurate, high-resolution sample inference from
amplicon sequencing data
dbplyr A 'dplyr' Back End for Databases
DECIPHER Tools for curating, analyzing, and manipulating
biological sequences
DeconRNASeq Deconvolution of Heterogeneous Tissue Samples
for mRNA-Seq data
DEGseq Identify Differentially Expressed Genes from
RNA-seq data
DelayedArray A unified framework for working transparently
with on-disk and in-memory array-like datasets
DelayedMatrixStats Functions that Apply to Rows and Columns of
'DelayedMatrix' Objects
dendextend Extending 'dendrogram' Functionality in R
derfinder Annotation-agnostic differential expression
analysis of RNA-seq data at base-pair
resolution via the DER Finder approach
derfinderHelper derfinder helper package
DESeq2 Differential gene expression analysis based on
the negative binomial distribution
DNAcopy DNA copy number data analysis
dqrng Fast Pseudo Random Number Generators
DRIMSeq Differential transcript usage and tuQTL
analyses with Dirichlet-multinomial model in
RNA-seq
DropletUtils Utilities for Handling Single-Cell Droplet Data
dupRadar Assessment of duplication rates in RNA-Seq
datasets
DynDoc Dynamic document tools
edgeR Empirical Analysis of Digital Gene Expression
Data in R
ensembldb Utilities to create and use Ensembl-based
annotation databases
ExperimentHub Client to access ExperimentHub resources
FDb.InfiniumMethylation.hg19
Annotation package for Illumina Infinium DNA
methylation probes
fgsea Fast Gene Set Enrichment Analysis
flock Process Synchronization Using File Locks
flowCore flowCore: Basic structures for flow cytometry
data
FlowSorted.Blood.EPIC Illumina EPIC data on immunomagnetic sorted
peripheral adult blood cells
FlowSorted.CordBloodCombined.450k
Illumina 450k/EPIC data on FACS and MACS
umbilical blood cells
fs Cross-Platform File System Operations Based on
'libuv'
gaston Genetic Data Handling (QC, GRM, LD, PCA) &
Linear Mixed Models
gcrma Background Adjustment Using Sequence
Information
gdsfmt R Interface to CoreArray Genomic Data Structure
(GDS) Files
genefilter genefilter: methods for filtering genes from
high-throughput experiments
geneLenDataBase Lengths of mRNA transcripts for a number of
genomes
geneplotter Graphics related functions for Bioconductor
GENESIS GENetic EStimation and Inference in Structured
samples (GENESIS): Statistical methods for
analyzing genetic data from samples with
population structure and/or relatedness
GENIE3 GEne Network Inference with Ensemble of trees
GenomeInfoDb Utilities for manipulating chromosome names,
including modifying them to follow a particular
naming style
GenomeInfoDbData Species and taxonomy ID look up tables used by
GenomeInfoDb
GenomicAlignments Representation and manipulation of short
genomic alignments
GenomicFeatures Conveniently import and query gene models
GenomicFiles Distributed computing by file or by range
GenomicRanges Representation and manipulation of genomic
intervals
GenomicScores Infrastructure to work with genomewide
position-specific scores
genoPlotR Plot Publication-Grade Gene and Genome Maps
genoset A RangedSummarizedExperiment with methods for
copy number analysis
GEOquery Get data from NCBI Gene Expression Omnibus
(GEO)
GGally Extension to 'ggplot2'
ggbeeswarm Categorical Scatter (Violin Point) Plots
ggbio Visualization tools for genomic data
ggfortify Data Visualization Tools for Statistical
Analysis Results
ggrepel Automatically Position Non-Overlapping Text
Labels with 'ggplot2'
Glimma Interactive HTML graphics
GlobalAncova Global test for groups of variables via model
comparisons
globaltest Testing Groups of Covariates/Features for
Association with a Response Variable, with
Applications to Gene Set Testing
GO.db A set of annotation maps describing the entire
Gene Ontology
goseq Gene Ontology analyser for RNA-seq and other
length biased data
GOstats Tools for manipulating GO and microarrays
graph graph: A package to handle graph data
structures
grImport2 Importing 'SVG' Graphics
GSA Gene Set Analysis
GSEABase Gene set enrichment data structures and methods
gsmoothr Smoothing tools
GSVA Gene Set Variation Analysis for microarray and
RNA-seq data
Gviz Plotting data and annotation information along
genomic coordinates
GWASExactHW Exact Hardy-Weinburg testing for Genome Wide
Association Studies
GWASTools Tools for Genome Wide Association Studies
HDF5Array HDF5 backend for DelayedArray objects
hgu133plus2.db Affymetrix Human Genome U133 Plus 2.0 Array
annotation data (chip hgu133plus2)
hierfstat Estimation and Tests of Hierarchical
F-Statistics
HMMcopy Copy number prediction with correction for GC
and mappability bias for HTS data
Homo.sapiens Annotation package for the Homo.sapiens object
IlluminaHumanMethylation450kanno.ilmn12.hg19
Annotation for Illumina's 450k methylation
arrays
IlluminaHumanMethylation450kmanifest
Annotation for Illumina's 450k methylation
arrays
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
Annotation for Illumina's EPIC methylation
arrays
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Annotation for Illumina's EPIC methylation
arrays
IlluminaHumanMethylationEPICmanifest
Manifest for Illumina's EPIC methylation arrays
illuminaio Parsing Illumina Microarray Output Files
impute impute: Imputation for microarray data
interactiveDisplayBase
Base package for enabling powerful shiny web
displays of Bioconductor objects
IRanges Foundation of integer range manipulation in
Bioconductor
KEGG.db A set of annotation maps for KEGG
KEGGgraph KEGGgraph: A graph approach to KEGG PATHWAY in
R and Bioconductor
KEGGprofile An annotation and visualization package for
multi-types and multi-groups expression data in
KEGG pathway
KEGGREST Client-side REST access to KEGG
label.switching Relabelling MCMC Outputs of Mixture Models
LEA LEA: an R package for Landscape and Ecological
Association Studies
limma Linear Models for Microarray Data
limSolve Solving Linear Inverse Models
lmerTest Tests in Linear Mixed Effects Models
lpsymphony Symphony integer linear programming solver in R
lumi BeadArray Specific Methods for Illumina
Methylation and Expression Microarrays
marray Exploratory analysis for two-color spotted
microarray data
maSigPro Significant Gene Expression Profile Differences
in Time Course Gene Expression Data
MEDIPS DNA IP-seq data analysis
memuse Memory Estimation Utilities
metagenomeSeq Statistical analysis for sparse high-throughput
sequencing
metaMA Meta-analysis for MicroArrays
methylumi Handle Illumina methylation data
minfi Analyze Illumina Infinium DNA methylation
arrays
mixOmics Omics Data Integration Project
mmapcharr Memory-Map Character Files
MotifDb An Annotated Collection of Protein-DNA Binding
Sequence Motifs
motifStack Plot stacked logos for single or multiple DNA,
RNA and amino acid sequence
MotIV Motif Identification and Validation
multtest Resampling-based multiple hypothesis testing
nabor Wraps 'libnabo', a Fast K Nearest Neighbour
Library for Low Dimensions
NADA Nondetects and Data Analysis for Environmental
Data
NOISeq Exploratory analysis and differential
expression for RNA-seq data
oligo Preprocessing tools for oligonucleotide arrays
oligoClasses Classes for high-throughput arrays supported by
oligo and crlmm
org.Hs.eg.db Genome wide annotation for Human
org.Mm.eg.db Genome wide annotation for Mouse
org.Rn.eg.db Genome wide annotation for Rat
org.Sc.sgd.db Genome wide annotation for Yeast
OrganismDbi Software to enable the smooth interfacing of
different database packages
pathview a tool set for pathway based data integration
and visualization
pcadapt Fast Principal Component Analysis for Outlier
Detection
pcaMethods A collection of PCA methods
pegas Population and Evolutionary Genetics Analysis
System
perm Exact or Asymptotic permutation tests
PFAM.db A set of protein ID mappings for PFAM
pheatmap Pretty Heatmaps
phyloseq Handling and analysis of high-throughput
microbiome census data
pinfsc50 Sequence ('FASTA'), Annotation ('GFF') and
Variants ('VCF') for 17 Samples of 'P.
Infestans" and 1 'P. Mirabilis'
pixmap Bitmap Images (``Pixel Maps'')
polyester Simulate RNA-seq reads
polysat Tools for Polyploid Microsatellite Analysis
pophelper Tabulate, analyse and visualise admixture
proportions from STRUCTURE, TESS, BAPS,
ADMIXTURE and tab-delimited q-matrices files
poppr Genetic Analysis of Populations with Mixed
Reproduction
preprocessCore A collection of pre-processing functions
progressr A Inclusive, Unifying API for Progress Updates
ProtGenerics S4 generic functions for Bioconductor
proteomics infrastructure
PureCN Copy number calling and SNV classification
using targeted short read sequencing
qiime2R qiime2R
quantsmooth Quantile smoothing and genomic visualization of
array data
qvalue Q-value estimation for false discovery rate
control
R.devices Unified Handling of Graphics Devices
rappdirs Application Directories: Determine Where to
Save Data, Caches, and Logs
RBGL An interface to the BOOST graph library
RcppAnnoy 'Rcpp' Bindings for 'Annoy', a Library for
Approximate Nearest Neighbors
RcppGSL 'Rcpp' Integration for 'GNU GSL' Vectors and
Matrices
RcppHNSW 'Rcpp' Bindings for 'hnswlib', a Library for
Approximate Nearest Neighbors
RcppZiggurat 'Rcpp' Integration of Different "Ziggurat"
Normal RNG Implementations
readr Read Rectangular Text Data
regioneR Association analysis of genomic regions based
on permutation tests
Repitools Epigenomic tools
ReportingTools Tools for making reports in various formats
Rfast A Collection of Efficient and Extremely Fast R
Functions
rGADEM de novo motif discovery
Rgraphviz Provides plotting capabilities for R graph
objects
rhdf5 R Interface to HDF5
Rhdf5lib hdf5 library as an R package
RhpcBLASctl Control the Number of Threads on 'BLAS'
Rhtslib HTSlib high-throughput sequencing library as an
R package
Ringo R Investigation of ChIP-chip Oligoarrays
rmio Provides 'mio' C++11 Header Files
RNASeqPower Sample size for RNAseq studies
ROC utilities for ROC, with microarray focus
RProtoBufLib C++ headers and static libraries of Protocol
buffers
Rsamtools Binary alignment (BAM), FASTA, variant call
(BCF), and tabix file import
Rsolnp General Non-Linear Optimization
Rsubread Subread Sequence Alignment and Counting for R
rsvd Randomized Singular Value Decomposition
rtracklayer R interface to genome annotation files and the
UCSC genome browser
S4Vectors Foundation of vector-like and list-like
containers in Bioconductor
samr SAM: Significance Analysis of Microarrays
scater Single-Cell Analysis Toolkit for Gene
Expression Data in R
scran Methods for Single-Cell RNA-Seq Data Analysis
scrime Analysis of High-Dimensional Categorical Data
Such as SNP Data
segmented Regression Models with Break-Points /
Change-Points Estimation
SeqArray Data management of large-scale whole-genome
sequence variant calls
seqinr Biological Sequences Retrieval and Analysis
seqLogo Sequence logos for DNA sequence alignments
SeqVarTools Tools for variant data
shinyFiles A Server-Side File System Viewer for Shiny
shinythemes Themes for Shiny
ShortRead FASTQ input and manipulation
sigaR Statistics for Integrative Genomics Analyses in
R
siggenes Multiple Testing using SAM and Efron's
Empirical Bayes Approaches
SingleCellExperiment S4 Classes for Single Cell Data
SingleR Reference-Based Single-Cell RNA-Seq Annotation
sitmo Parallel Pseudo Random Number Generator (PPRNG)
'sitmo' Header Files
SMVar Structural Model for variances
SNPRelate Parallel Computing Toolset for Relatedness and
Principal Component Analysis of SNP Data
SPIA Signaling Pathway Impact Analysis (SPIA) using
combined evidence of pathway
over-representation and unusual signaling
perturbations
splitstackshape Stack and Reshape Datasets After Splitting
Concatenated Values
SSPA General Sample Size and Power Analysis for
Microarray and Next-Generation Sequencing Data
stageR stageR: stage-wise analysis of high throughput
gene expression data in R
SummarizedExperiment SummarizedExperiment container
sva Surrogate Variable Analysis
TeachingDemos Demonstrations for Teaching and Learning
truncnorm Truncated Normal Distribution
TxDb.Hsapiens.UCSC.hg19.knownGene
Annotation package for TxDb object(s)
TxDb.Mmusculus.UCSC.mm10.knownGene
Annotation package for TxDb object(s)
tximport Import and summarize transcript-level estimates
for transcript- and gene-level analysis
variancePartition Quantify and interpret divers of variation in
multilevel gene expression experiments
VariantAnnotation Annotation of Genetic Variants
vcfR Manipulate and Visualize VCF Data
venn Draw Venn Diagrams
vipor Plot Categorical Data Using Quasirandom Noise
and Density Estimates
vsn Variance stabilization and calibration for
microarray data
wateRmelon Illumina 450 methylation array normalization
and metrics
Wrench Wrench normalization for sparse count data
xgboost Extreme Gradient Boosting
xml2 Parse XML
XVector Foundation of external vector representation
and manipulation in Bioconductor
zCompositions Treatment of Zeros, Left-Censored and Missing
Values in Compositional Data Sets
zlibbioc An R packaged zlib-1.2.5
Packages in library ‘/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/R-Geo/4.0.1-gimkl-2020a’:
DCluster Functions for the Detection of Spatial Clusters
of Diseases
gdistance Distances and Routes on Geographical Grids
gstat Spatial and Spatio-Temporal Geostatistical
Modelling, Prediction and Simulation
ipdw Spatial Interpolation by Inverse Path Distance
Weighting
rgdal Bindings for the 'Geospatial' Data Abstraction
Library
rgeos Interface to Geometry Engine - Open Source
('GEOS')
sf Simple Features for R
spacetime Classes and Methods for Spatio-Temporal Data
spdep Spatial Dependence: Weighting Schemes,
Statistics
units Measurement Units for R Vectors
Packages in library ‘/scale_wlg_persistent/filesets/home/hugh.cross/R/x86_64-pc-linux-gnu-library/4.0’:
BH Boost C++ Header Files
Biobase Biobase: Base functions for Bioconductor
BiocGenerics S4 generic functions used in Bioconductor
BiocParallel Bioconductor facilities for parallel evaluation
BiocVersion Set the appropriate version of Bioconductor
packages
Biostrings Efficient manipulation of biological strings
brio Basic R Input Output
cachem Cache R Objects with Automatic Pruning
callr Call R from R
cli Helpers for Developing Command Line Interfaces
colorspace A Toolbox for Manipulating and Assessing Colors
and Palettes
commonmark High Performance CommonMark and Github Markdown
Rendering in R
cowsay Messages, Warnings, Strings with Ascii Animals
crayon Colored Terminal Output
credentials Tools for Managing SSH and Git Credentials
dada2 Accurate, high-resolution sample inference from
amplicon sequencing data
DelayedArray A unified framework for working transparently
with on-disk and in-memory array-like datasets
desc Manipulate DESCRIPTION Files
devtools Tools to Make Developing R Packages Easier
diffobj Diffs for R Objects
digest Create Compact Hash Digests of R Objects
fansi ANSI Control Sequence Aware String Functions
farver High Performance Colour Space Manipulation
formatR Format R Code Automatically
fortunes R Fortunes
fs Cross-Platform File System Operations Based on
'libuv'
GenomeInfoDb Utilities for manipulating chromosome names,
including modifying them to follow a particular
naming style
GenomeInfoDbData Species and taxonomy ID look up tables used by
GenomeInfoDb
GenomicAlignments Representation and manipulation of short
genomic alignments
GenomicRanges Representation and manipulation of genomic
intervals
gert Simple Git Client for R
ggplot2 Create Elegant Data Visualisations Using the
Grammar of Graphics
gh 'GitHub' 'API'
gitcreds Query 'git' Credentials from 'R'
glue Interpreted String Literals
httr Tools for Working with URLs and HTTP
ini Read and Write '.ini' Files
IRanges Foundation of integer range manipulation in
Bioconductor
isoband Generate Isolines and Isobands from Regularly
Spaced Elevation Grids
jsonlite A Simple and Robust JSON Parser and Generator
for R
labeling Axis Labeling
lifecycle Manage the Life Cycle of your Package Functions
magrittr A Forward-Pipe Operator for R
MatrixGenerics S4 Generic Summary Statistic Functions that
Operate on Matrix-Like Objects
matrixStats Functions that Apply to Rows and Columns of
Matrices (and to Vectors)
memoise Memoisation of Functions
pillar Coloured Formatting for Columns
pkgbuild Find Tools Needed to Build R Packages
pkgload Simulate Package Installation and Attach
processx Execute and Control System Processes
ps List, Query, Manipulate System Processes
R6 Encapsulated Classes with Reference Semantics
rappdirs Application Directories: Determine Where to
Save Data, Caches, and Logs
rcmdcheck Run 'R CMD check' from 'R' and Capture Results
Rcpp Seamless R and C++ Integration
RcppParallel Parallel Programming Tools for 'Rcpp'
RCurl General Network (HTTP/FTP/...) Client Interface
for R
rematch2 Tidy Output from Regular Expression Matching
remotes R Package Installation from Remote
Repositories, Including 'GitHub'
Rhtslib HTSlib high-throughput sequencing library as an
R package
rlang Functions for Base Types and Core R and
'Tidyverse' Features
rmsfact Amazing Random Facts About the World's Greatest
Hacker
roxygen2 In-Line Documentation for R
Rsamtools Binary alignment (BAM), FASTA, variant call
(BCF), and tabix file import
rstudioapi Safely Access the RStudio API
rversions Query 'R' Versions, Including 'r-release' and
'r-oldrel'
S4Vectors Foundation of vector-like and list-like
containers in Bioconductor
sessioninfo R Session Information
ShortRead FASTQ input and manipulation
stringi Character String Processing Facilities
SummarizedExperiment SummarizedExperiment container
testthat Unit Testing for R
tibble Simple Data Frames
usethis Automate Package and Project Setup
utf8 Unicode Text Processing
vctrs Vector Helpers
viridisLite Colorblind-Friendly Color Maps (Lite Version)
waldo Find Differences Between R Objects
whisker {{mustache}} for R, Logicless Templating
withr Run Code 'With' Temporarily Modified Global
State
xml2 Parse XML
xopen Open System Files, 'URLs', Anything
XVector Foundation of external vector representation
and manipulation in Bioconductor
zip Cross-Platform 'zip' Compression
zlibbioc An R packaged zlib-1.2.5
Packages in library ‘/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/R/4.0.1-gimkl-2020a/lib64/R/library’:
abind Combine Multidimensional Arrays
acepack ACE and AVAS for Selecting Multiple Regression
Transformations
akima Interpolation of Irregularly and Regularly
Spaced Data
ape Analyses of Phylogenetics and Evolution
askpass Safe Password Entry for R, Git, and SSH
assertthat Easy Pre and Post Assertions
backports Reimplementations of Functions Introduced Since
R-3.0.0
base The R Base Package
base64 Base64 Encoder and Decoder
base64enc Tools for base64 encoding
BB Solving and Optimizing Large-Scale Nonlinear
Systems
BBmisc Miscellaneous Helper Functions for B. Bischl
beanplot Visualization via Beanplots (like
Boxplot/Stripchart/Violin Plot)
betapart Partitioning Beta Diversity into Turnover and
Nestedness Components
BH Boost C++ Header Files
BiasedUrn Biased Urn Model Distributions
bibtex Bibtex Parser
bindr Parametrized Active Bindings
bindrcpp An 'Rcpp' Interface to Active Bindings
BiocManager Access the Bioconductor Project Package
Repository
bit A Class for Vectors of 1-Bit Booleans
bit64 A S3 Class for Vectors of 64bit Integers
bitops Bitwise Operations
blob A Simple S3 Class for Representing Vectors of
Binary Data ('BLOBS')
boot Bootstrap Functions (Originally by Angelo Canty
for S)
brew Templating Framework for Report Generation
brglm Bias Reduction in Binomial-Response Generalized
Linear Models
broom Convert Statistical Analysis Objects into Tidy
Tibbles
calibrate Calibration of Scatterplot and Biplot Axes
callr Call R from R
car Companion to Applied Regression
carData Companion to Applied Regression Data Sets
caTools Tools: Moving Window Statistics, GIF, Base64,
ROC AUC, etc
cellranger Translate Spreadsheet Cell Ranges to Rows and
Columns
checkmate Fast and Versatile Argument Checks
chron Chronological Objects which can Handle Dates
and Times
class Functions for Classification
classInt Choose Univariate Class Intervals
cli Helpers for Developing Command Line Interfaces
clipr Read and Write from the System Clipboard
cluster "Finding Groups in Data": Cluster Analysis
Extended Rousseeuw et al.
coda Output Analysis and Diagnostics for MCMC
codetools Code Analysis Tools for R
colorspace A Toolbox for Manipulating and Assessing Colors
and Palettes
compiler The R Compiler Package
corpcor Efficient Estimation of Covariance and
(Partial) Correlation
crayon Colored Terminal Output
crosstalk Inter-Widget Interactivity for HTML Widgets
crs Categorical Regression Splines
cubature Adaptive Multivariate Integration over
Hypercubes
curl A Modern and Flexible Web Client for R
data.table Extension of `data.frame`
datasets The R Datasets Package
DBI R Database Interface
deldir Delaunay Triangulation and Dirichlet (Voronoi)
Tessellation
DEoptimR Differential Evolution Optimization in Pure R
desc Manipulate DESCRIPTION Files
deSolve Solvers for Initial Value Problems of
Differential Equations ('ODE', 'DAE', 'DDE')
dichromat Color Schemes for Dichromats
digest Create Compact Hash Digests of R Objects
dismo Species Distribution Modeling
doMC Foreach Parallel Adaptor for 'parallel'
doMPI Foreach Parallel Adaptor for the Rmpi Package
doParallel Foreach Parallel Adaptor for the 'parallel'
Package
doRNG Generic Reproducible Parallel Backend for
'foreach' Loops
dotCall64 Enhanced Foreign Function Interface Supporting
Long Vectors
dplyr A Grammar of Data Manipulation
e1071 Misc Functions of the Department of Statistics,
Probability Theory Group (Formerly: E1071), TU
Wien
ellipse Functions for Drawing Ellipses and Ellipse-Like
Confidence Regions
ellipsis Tools for Working with ...
evaluate Parsing and Evaluation Tools that Provide More
Details than the Default
expm Matrix Exponential, Log, 'etc'
fail File Abstraction Interface Layer (FAIL)
fansi ANSI Control Sequence Aware String Functions
farver High Performance Colour Space Manipulation
fastcluster Fast Hierarchical Clustering Routines for R and
'Python'
fastICA FastICA Algorithms to Perform ICA and
Projection Pursuit
fastmap Fast Implementation of a Key-Value Store
fastmatch Fast match() function
ff Memory-Efficient Storage of Large Data on Disk
and Fast Access Functions
float 32-Bit Floats
FNN Fast Nearest Neighbor Search Algorithms and
Applications
forcats Tools for Working with Categorical Variables
(Factors)
foreach Provides Foreach Looping Construct
foreign Read Data Stored by 'Minitab', 'S', 'SAS',
'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...
formatR Format R Code Automatically
Formula Extended Model Formulas
futile.logger A Logging Utility for R
futile.options Futile Options Management
gam Generalized Additive Models
gamlss Generalised Additive Models for Location Scale
and Shape
gamlss.data GAMLSS Data
gamlss.dist Distributions for Generalized Additive Models
for Location Scale and Shape
gbm Generalized Boosted Regression Models
gdata Various R Programming Tools for Data
Manipulation
generics Common S3 Generics not Provided by Base R
Methods Related to Model Fitting
geometry Mesh Generation and Surface Tessellation
getopt C-Like 'getopt' Behavior
ggplot2 Create Elegant Data Visualisations Using the
Grammar of Graphics
glmmML Generalized Linear Models with Clustering
glmnet Lasso and Elastic-Net Regularized Generalized
Linear Models
glue Interpreted String Literals
gmodels Various R Programming Tools for Model Fitting
goftest Classical Goodness-of-Fit Tests for Univariate
Distributions
gplots Various R Programming Tools for Plotting Data
graphics The R Graphics Package
grDevices The R Graphics Devices and Support for Colours
and Fonts
grid The Grid Graphics Package
gridBase Integration of base and grid graphics
gridExtra Miscellaneous Functions for "Grid" Graphics
gsalib Utility Functions For GATK
gtable Arrange 'Grobs' in Tables
gtools Various R Programming Tools
haven Import and Export 'SPSS', 'Stata' and 'SAS'
Files
highr Syntax Highlighting for R Source Code
Hmisc Harrell Miscellaneous
hms Pretty Time of Day
htmlTable Advanced Tables for Markdown/HTML
htmltools Tools for HTML
htmlwidgets HTML Widgets for R
httpuv HTTP and WebSocket Server Library
httr Tools for Working with URLs and HTTP
hwriter HTML Writer - Outputs R objects in HTML format
igraph Network Analysis and Visualization
inline Functions to Inline C, C++, Fortran Function
Calls from R
intervals Tools for Working with Points and Intervals
irace Iterated Racing for Automatic Algorithm
Configuration
irlba Fast Truncated Singular Value Decomposition and
Principal Components Analysis for Large Dense
and Sparse Matrices
isoband Generate Isolines and Isobands from Regularly
Spaced Elevation Grids
iterators Provides Iterator Construct
itertools Iterator Tools
jomo Multilevel Joint Modelling Multiple Imputation
jpeg Read and write JPEG images
jsonlite A Robust, High Performance JSON Parser and
Generator for R
KernSmooth Functions for Kernel Smoothing Supporting Wand
& Jones (1995)
knitr A General-Purpose Package for Dynamic Report
Generation in R
labeling Axis Labeling
lambda.r Modeling Data with Functional Programming
later Utilities for Scheduling Functions to Execute
Later with Event Loops
lattice Trellis Graphics for R
latticeExtra Extra Graphical Utilities Based on Lattice
lazyeval Lazy (Non-Standard) Evaluation
LearnBayes Functions for Learning Bayesian Inference
lifecycle Manage the Life Cycle of your Package Functions
linprog Linear Programming / Optimization
lme4 Linear Mixed-Effects Models using 'Eigen' and
S4
lmtest Testing Linear Regression Models
locfit Local Regression, Likelihood and Density
Estimation
logistf Firth's Bias-Reduced Logistic Regression
logspline Routines for Logspline Density Estimation
loo Efficient Leave-One-Out Cross-Validation and
WAIC for Bayesian Models
lpSolve Interface to 'Lp_solve' v. 5.5 to Solve
Linear/Integer Programs
magic Create and Investigate Magic Squares
magrittr A Forward-Pipe Operator for R
manipulateWidget Add Even More Interactivity to Interactive
Charts
maptools Tools for Handling Spatial Objects
markdown Render Markdown with the C Library 'Sundown'
MASS Support Functions and Datasets for Venables and
Ripley's MASS
Matrix Sparse and Dense Matrix Classes and Methods
MatrixModels Modelling with Sparse And Dense Matrices
matrixStats Functions that Apply to Rows and Columns of
Matrices (and to Vectors)
mclust Gaussian Mixture Modelling for Model-Based
Clustering, Classification, and Density
Estimation
MCMCglmm MCMC Generalised Linear Mixed Models
memoise Memoisation of Functions
methods Formal Methods and Classes
mgcv Mixed GAM Computation Vehicle with Automatic
Smoothness Estimation
mice Multivariate Imputation by Chained Equations
mime Map Filenames to MIME Types
miniUI Shiny UI Widgets for Small Screens
minqa Derivative-free optimization algorithms by
quadratic approximation
mitml Tools for Multiple Imputation in Multilevel
Modeling
mitools Tools for Multiple Imputation of Missing Data
mnormt The Multivariate Normal and t Distributions,
and Their Truncated Versions
munsell Utilities for Using Munsell Colours
mvtnorm Multivariate Normal and t Distributions
neuRosim Functions to Generate fMRI Data Including
Activated Data, Noise Data and Resting State
Data
nleqslv Solve Systems of Nonlinear Equations
nlme Linear and Nonlinear Mixed Effects Models
nloptr R Interface to NLopt
nnet Feed-Forward Neural Networks and Multinomial
Log-Linear Models
nnls The Lawson-Hanson algorithm for non-negative
least squares (NNLS)
nor1mix Normal aka Gaussian (1-d) Mixture Models (S3
Classes and Methods)
np Nonparametric Kernel Smoothing Methods for
Mixed Data Types
numDeriv Accurate Numerical Derivatives
openssl Toolkit for Encryption, Signatures and
Certificates Based on OpenSSL
openxlsx Read, Write and Edit xlsx Files
optparse Command Line Option Parser
ordinal Regression Models for Ordinal Data
pan Multiple Imputation for Multivariate Panel or
Clustered Data
parallel Support for Parallel computation in R
pbdMPI Programming with Big Data -- Interface to MPI
pbkrtest Parametric Bootstrap and Kenward Roger Based
Methods for Mixed Model Comparison
penalized L1 (Lasso and Fused Lasso) and L2 (Ridge)
Penalized Estimation in GLMs and in the Cox
Model
perm Exact or Asymptotic permutation tests
permute Functions for Generating Restricted
Permutations of Data
phangorn Phylogenetic Reconstruction and Analysis
picante Integrating Phylogenies and Ecology
pillar Coloured Formatting for Columns
pkgbuild Find Tools Needed to Build R Packages
pkgconfig Private Configuration for 'R' Packages
pkgload Simulate Package Installation and Attach
pkgmaker Development Utilities for R Packages
plogr The 'plog' C++ Logging Library
plyr Tools for Splitting, Applying and Combining
Data
png Read and write PNG images
polyclip Polygon Clipping
praise Praise Users
prettyunits Pretty, Human Readable Formatting of Quantities
processx Execute and Control System Processes
profileModel Profiling Inference Functions for Various Model
Classes
profvis Interactive Visualizations for Profiling R Code
progress Terminal Progress Bars
promises Abstractions for Promise-Based Asynchronous
Programming
proto Prototype Object-Based Programming
ps List, Query, Manipulate System Processes
pscl Political Science Computational Laboratory
purrr Functional Programming Tools
quadprog Functions to Solve Quadratic Programming
Problems
quantreg Quantile Regression
R.methodsS3 S3 Methods Simplified
R.oo R Object-Oriented Programming with or without
References
R.utils Various Programming Utilities
R2OpenBUGS Running OpenBUGS from R
R6 Encapsulated Classes with Reference Semantics
RandomFields Simulation and Analysis of Random Fields
RandomFieldsUtils Utilities for the Simulation and Analysis of
Random Fields
randomForest Breiman and Cutler's Random Forests for
Classification and Regression
rARPACK Solvers for Large Scale Eigenvalue and SVD
Problems
raster Geographic Data Analysis and Modeling
rcdd Computational Geometry
RColorBrewer ColorBrewer Palettes
Rcpp Seamless R and C++ Integration
RcppArmadillo 'Rcpp' Integration for the 'Armadillo'
Templated Linear Algebra Library
RcppEigen 'Rcpp' Integration for the 'Eigen' Templated
Linear Algebra Library
RcppParallel Parallel Programming Tools for 'Rcpp'
RcppProgress An Interruptible Progress Bar with OpenMP
Support for C++ in R Packages
RCurl General Network (HTTP/FTP/...) Client Interface
for R
readr Read Rectangular Text Data
readxl Read Excel Files
registry Infrastructure for R Package Registries
rematch Match Regular Expressions with a Nicer 'API'
reshape Flexibly Reshape Data
reshape2 Flexibly Reshape Data: A Reboot of the Reshape
Package
rgl 3D Visualization Using OpenGL
rio A Swiss-Army Knife for Data I/O
rJava Low-Level R to Java Interface
rlang Functions for Base Types and Core R and
'Tidyverse' Features
rlecuyer R Interface to RNG with Multiple Streams
Rmpi Interface (Wrapper) to MPI (Message-Passing
Interface)
rngtools Utility Functions for Working with Random
Number Generators
robustbase Basic Robust Statistics
rpart Recursive Partitioning and Regression Trees
rprojroot Finding Files in Project Subdirectories
rrBLUP Ridge Regression and Other Kernels for Genomic
Selection
RSpectra Solvers for Large-Scale Eigenvalue and SVD
Problems
RSQLite 'SQLite' Interface for R
rstan R Interface to Stan
rstudioapi Safely Access the RStudio API
sandwich Robust Covariance Matrix Estimators
scales Scale Functions for Visualization
sendmailR send email using R
sfsmisc Utilities from 'Seminar fuer Statistik' ETH
Zurich
shape Functions for Plotting Graphical Shapes, Colors
shiny Web Application Framework for R
snow Simple Network of Workstations
snowfall Easier cluster computing (based on snow).
sourcetools Tools for Reading, Tokenizing and Parsing R
Code
sp Classes and Methods for Spatial Data
spam SPArse Matrix
SparseM Sparse Linear Algebra
spatial Functions for Kriging and Point Pattern
Analysis
spatstat Spatial Point Pattern Analysis, Model-Fitting,
Simulation, Tests
spatstat.data Datasets for 'spatstat'
spatstat.utils Utility Functions for 'spatstat'
spData Datasets for Spatial Analysis
spgrass6 Interface Between GRASS 6+ Geographical
Information System and R
splancs Spatial and Space-Time Point Pattern Analysis
splines Regression Spline Functions and Classes
StanHeaders C++ Header Files for Stan
statmod Statistical Modeling
stats The R Stats Package
stats4 Statistical Functions using S4 Classes
stringi Character String Processing Facilities
stringr Simple, Consistent Wrappers for Common String
Operations
survey Analysis of Complex Survey Samples
survival Survival Analysis
sys Powerful and Reliable Tools for Running System
Commands in R
tcltk Tcl/Tk Interface
tensor Tensor product of arrays
tensorA Advanced Tensor Arithmetic with Named Indices
testthat Unit Testing for R
tibble Simple Data Frames
tidyr Tidy Messy Data
tidyselect Select from a Set of Strings
tmvnsim Truncated Multivariate Normal Simulation
tools Tools for Package Development
tseriesChaos Analysis of Nonlinear Time Series
ucminf General-Purpose Unconstrained Non-Linear
Optimization
utf8 Unicode Text Processing
utils The R Utils Package
vcd Visualizing Categorical Data
vctrs Vector Helpers
vegan Community Ecology Package
VGAM Vector Generalized Linear and Additive Models
viridis Default Color Maps from 'matplotlib'
viridisLite Default Color Maps from 'matplotlib' (Lite
Version)
waveslim Basic Wavelet Routines for One-, Two-, and
Three-Dimensional Signal Processing
webshot Take Screenshots of Web Pages
withr Run Code 'With' Temporarily Modified Global
State
xfun Miscellaneous Functions by 'Yihui Xie'
XML Tools for Parsing and Generating XML Within R
and S-Plus
xtable Export Tables to LaTeX or HTML
xts eXtensible Time Series
yaml Methods to Convert R Data to YAML and Back
zeallot Multiple, Unpacking, and Destructuring
Assignment
zip Cross-Platform 'zip' Compression
zoo S3 Infrastructure for Regular and Irregular
Time Series (Z's Ordered Observations)