R Packagesยง
We provide a collection of installed R packages for each release of R, as a bundle module. This page lists the packages for the current recommended R bundle.
This can be loaded using:
module load r/recommended
The version of R provided with this bundle is currently R version 3.6.0 (2019-04-26).
The following list was last updated at: 15:32:24 (+0000) on 02 Feb 2021.
| Module | Version | Description |
|---|---|---|
AnnotationForge |
1.26.0 | Tools for building SQLite-based annotation data packages |
BiocManager |
1.30.4 | Access the Bioconductor Project Package Repository |
BiocVersion |
3.9.0 | Set the appropriate version of Bioconductor packages |
Deriv |
3.8.5 | Symbolic Differentiation |
dgo |
0.2.15 | Dynamic Estimation of Group-Level Opinion |
dgodata |
0.0.2 | Data for the 'dgo' Package |
digest |
0.6.21 | Create Compact Hash Digests of R Objects |
GO.db |
3.8.2 | A set of annotation maps describing the entire Gene Ontology |
hgu95av2.db |
3.2.3 | Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) |
HKprocess |
0.0-2 | Hurst-Kolmogorov Process |
hugene10stprobeset.db |
8.7.0 | Affymetrix hugene10 annotation data (chip hugene10stprobeset) |
hugene10sttranscriptcluster.db |
8.7.0 | Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) |
Illumina450ProbeVariants.db |
1.20.0 | Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes |
IlluminaHumanMethylation450kmanifest |
0.4.0 | Annotation for Illumina's 450k methylation arrays |
illuminaHumanv4.db |
1.26.0 | Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) |
INLA |
19.09.03 | Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations |
KEGG.db |
3.2.3 | A set of annotation maps for KEGG |
MCMCpack |
1.4-4 | Markov Chain Monte Carlo (MCMC) Package |
missMethyl |
1.18.0 | Analysing Illumina HumanMethylation BeadChip Data |
org.Hs.eg.db |
3.8.2 | Genome wide annotation for Human |
orthopolynom |
1.0-5 | Collection of functions for orthogonal and orthonormal polynomials |
polynom |
1.4-0 | A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations |
quanteda.corpora |
0.87 | A collection of corpora for quanteda |
RcppZiggurat |
0.1.5 | 'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations |
Rfast |
1.9.9 | A Collection of Efficient and Extremely Fast R Functions |
sf |
0.7-7 | Simple Features for R |
splancs |
2.01-40 | Spatial and Space-Time Point Pattern Analysis |
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 |
adapt |
1.0-4 | adapt -- multidimensional numerical integration |
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 |
ADGofTest |
0.3 | Anderson-Darling GoF test |
affxparser |
1.56.0 | Affymetrix File Parsing SDK |
affy |
1.62.0 | Methods for Affymetrix Oligonucleotide Arrays |
affydata |
1.32.0 | Affymetrix Data for Demonstration Purpose |
affyio |
1.54.0 | Tools for parsing Affymetrix data files |
affylmGUI |
1.58.0 | GUI for limma Package with Affymetrix Microarrays |
affyPLM |
1.60.0 | Methods for fitting probe-level models |
affyQCReport |
1.62.0 | QC Report Generation for affyBatch objects |
akima |
0.6-2 | Interpolation of Irregularly and Regularly Spaced Data |
annaffy |
1.56.0 | Annotation tools for Affymetrix biological metadata |
annmap |
1.26.0 | Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis. |
annotate |
1.62.0 | Annotation for microarrays |
AnnotationDbi |
1.46.0 | Manipulation of SQLite-based annotations in Bioconductor |
AnnotationFilter |
1.8.0 | Facilities for Filtering Bioconductor Annotation Resources |
ape |
5.3 | Analyses of Phylogenetics and Evolution |
arm |
1.10-1 | Data Analysis Using Regression and Multilevel/Hierarchical Models |
aroma.affymetrix |
3.2.0 | Analysis of Large Affymetrix Microarray Data Sets |
aroma.apd |
0.6.0 | A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated] |
aroma.core |
3.2.0 | Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework |
aroma.light |
3.14.0 | Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types |
askpass |
1.1 | Safe Password Entry for R, Git, and SSH |
assertthat |
0.2.1 | Easy Pre and Post Assertions |
backports |
1.1.4 | Reimplementations of Functions Introduced Since R-3.0.0 |
base |
3.6.0 | The R Base Package |
base64 |
2.0 | Base64 Encoder and Decoder |
base64enc |
0.1-3 | Tools for base64 encoding |
BaSTA |
1.9.4 | Age-Specific Survival Analysis from Incomplete Capture-Recapture/Recovery Data |
BatchJobs |
1.8 | Batch Computing with R |
bayesplot |
1.7.0 | Plotting for Bayesian Models |
BBmisc |
1.11 | Miscellaneous Helper Functions for B. Bischl |
beachmat |
2.0.0 | Compiling Bioconductor to Handle Each Matrix Type |
beadarray |
2.34.0 | Quality assessment and low-level analysis for Illumina BeadArray data |
beadarrayExampleData |
1.22.0 | Example data for the beadarray package |
BeadDataPackR |
1.36.0 | Compression of Illumina BeadArray data |
beanplot |
1.2 | Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot) |
BH |
1.69.0-1 | Boost C++ Header Files |
BiasedUrn |
1.07 | Biased Urn Model Distributions |
bibtex |
0.4.2 | Bibtex Parser |
bio3d |
2.3-4 | Biological Structure Analysis |
Biobase |
2.44.0 | Biobase: Base functions for Bioconductor |
BiocFileCache |
1.8.0 | Manage Files Across Sessions |
BiocGenerics |
0.30.0 | S4 generic functions used in Bioconductor |
BiocParallel |
1.18.0 | Bioconductor facilities for parallel evaluation |
biomaRt |
2.40.1 | Interface to BioMart databases (i.e. Ensembl) |
Biostrings |
2.52.0 | Efficient manipulation of biological strings |
biovizBase |
1.32.0 | Basic graphic utilities for visualization of genomic data. |
bit |
1.1-14 | A Class for Vectors of 1-Bit Booleans |
bit64 |
0.9-7 | A S3 Class for Vectors of 64bit Integers |
bitops |
1.0-6 | Bitwise Operations |
blob |
1.1.1 | A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS') |
blockmodeling |
0.3.4 | Generalized and Classical Blockmodeling of Valued Networks |
boot |
1.3-22 | Bootstrap Functions (Originally by Angelo Canty for S) |
brew |
1.0-6 | Templating Framework for Report Generation |
broom |
0.5.2 | Convert Statistical Analysis Objects into Tidy Tibbles |
BSgenome |
1.52.0 | Software infrastructure for efficient representation of full genomes and their SNPs |
BSgenome.Hsapiens.UCSC.hg19 |
1.4.0 | Full genome sequences for Homo sapiens (UCSC version hg19) |
bsseq |
1.20.0 | Analyze, manage and store bisulfite sequencing data |
bumphunter |
1.26.0 | Bump Hunter |
callr |
3.2.0 | Call R from R |
car |
3.0-3 | Companion to Applied Regression |
carData |
3.0-2 | Companion to Applied Regression Data Sets |
caret |
6.0-84 | Classification and Regression Training |
Category |
2.50.0 | Category Analysis |
caTools |
1.17.1.2 | Tools: moving window statistics, GIF, Base64, ROC AUC, etc. |
CDM |
7.3-17 | Cognitive Diagnosis Modeling |
cellranger |
1.1.0 | Translate Spreadsheet Cell Ranges to Rows and Columns |
ChAMP |
2.14.0 | Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC |
ChAMPdata |
2.16.0 | Data Packages for ChAMP package |
checkmate |
1.9.4 | Fast and Versatile Argument Checks |
class |
7.3-15 | Functions for Classification |
classInt |
0.3-3 | Choose Univariate Class Intervals |
cli |
1.1.0 | Helpers for Developing Command Line Interfaces |
clipr |
0.6.0 | Read and Write from the System Clipboard |
clisymbols |
1.2.0 | Unicode Symbols at the R Prompt |
clue |
0.3-57 | Cluster Ensembles |
cluster |
2.0.8 | "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al. |
cmprsk |
2.2-8 | Subdistribution Analysis of Competing Risks |
coda |
0.19-3 | Output Analysis and Diagnostics for MCMC |
codetools |
0.2-16 | Code Analysis Tools for R |
colorRamps |
2.3 | Builds color tables |
colorspace |
1.4-1 | A Toolbox for Manipulating and Assessing Colors and Palettes |
colourpicker |
1.0 | A Colour Picker Tool for Shiny and for Selecting Colours in Plots |
combinat |
0.0-8 | combinatorics utilities |
compiler |
3.6.0 | The R Compiler Package |
copula |
0.999-19.1 | Multivariate Dependence with Copulas |
copynumber |
1.24.0 | Segmentation of single- and multi-track copy number data by penalized least squares regression. |
corpcor |
1.6.9 | Efficient Estimation of Covariance and (Partial) Correlation |
corrplot |
0.84 | Visualization of a Correlation Matrix |
crayon |
1.3.4 | Colored Terminal Output |
crosstalk |
1.0.0 | Inter-Widget Interactivity for HTML Widgets |
curl |
3.3 | A Modern and Flexible Web Client for R |
data.table |
1.12.2 | Extension of data.frame |
datasets |
3.6.0 | The R Datasets Package |
DBI |
1.0.0 | R Database Interface |
dbplyr |
1.4.0 | A 'dplyr' Back End for Databases |
DelayedArray |
0.10.0 | A unified framework for working transparently with on-disk and in-memory array-like datasets |
DelayedMatrixStats |
1.6.0 | Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects |
deldir |
0.1-16 | Delaunay Triangulation and Dirichlet (Voronoi) Tessellation |
dendextend |
1.12.0 | Extending 'dendrogram' Functionality in R |
DEoptimR |
1.0-8 | Differential Evolution Optimization in Pure R |
desc |
1.2.0 | Manipulate DESCRIPTION Files |
DESeq |
1.36.0 | Differential gene expression analysis based on the negative binomial distribution |
DESeq2 |
1.24.0 | Differential gene expression analysis based on the negative binomial distribution |
Design |
2.3-0 | Design Package |
devtools |
2.0.2 | Tools to Make Developing R Packages Easier |
DEXSeq |
1.30.0 | Inference of differential exon usage in RNA-Seq |
dichromat |
2.0-0 | Color Schemes for Dichromats |
digest |
0.6.20 | Create Compact Hash Digests of R Objects |
diptest |
0.75-7 | Hartigan's Dip Test Statistic for Unimodality - Corrected |
distr |
2.8.0 | Object Oriented Implementation of Distributions |
distrEx |
2.8.0 | Extensions of Package 'distr' |
DMRcate |
1.20.0 | Methylation array and sequencing spatial analysis methods |
DMRcatedata |
1.20.0 | Data Package for DMRcate package |
DNAcopy |
1.58.0 | DNA copy number data analysis |
doMC |
1.3.5 | Foreach Parallel Adaptor for 'parallel' |
doParallel |
1.0.14 | Foreach Parallel Adaptor for the 'parallel' Package |
doRNG |
1.7.1 | Generic Reproducible Parallel Backend for 'foreach' Loops |
dotCall64 |
1.0-0 | Enhanced Foreign Function Interface Supporting Long Vectors |
dplyr |
0.8.1 | A Grammar of Data Manipulation |
DSS |
2.32.0 | Dispersion shrinkage for sequencing data |
DT |
0.6 | A Wrapper of the JavaScript Library 'DataTables' |
dygraphs |
1.1.1.6 | Interface to 'Dygraphs' Interactive Time Series Charting Library |
dynamicTreeCut |
1.63-1 | Methods for Detection of Clusters in Hierarchical Clustering Dendrograms |
DynDoc |
1.62.0 | Dynamic document tools |
e1071 |
1.7-2 | Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien |
easyRNASeq |
2.20.0 | Count summarization and normalization for RNA-Seq data |
EBSeq |
1.24.0 | An R package for gene and isoform differential expression analysis of RNA-seq data |
edgeR |
3.26.5 | Empirical Analysis of Digital Gene Expression Data in R |
effects |
4.1-1 | Effect Displays for Linear, Generalized Linear, and Other Models |
ellipse |
0.4.1 | Functions for Drawing Ellipses and Ellipse-Like Confidence Regions |
ellipsis |
0.1.0 | Tools for Working with ... |
ensembldb |
2.8.0 | Utilities to create and use Ensembl-based annotation databases |
Epi |
2.37 | A Package for Statistical Analysis in Epidemiology |
erer |
2.5 | Empirical Research in Economics with R |
estimability |
1.3 | Tools for Assessing Estimability of Linear Predictions |
etm |
1.0.5 | Empirical Transition Matrix |
evaluate |
0.14 | Parsing and Evaluation Tools that Provide More Details than the Default |
evd |
2.3-3 | Functions for Extreme Value Distributions |
expm |
0.999-4 | Matrix Exponential, Log, 'etc' |
extrafont |
0.17 | Tools for using fonts |
extrafontdb |
1.0 | Package for holding the database for the extrafont package |
FactoMineR |
1.42 | Multivariate Exploratory Data Analysis and Data Mining |
fail |
1.3 | File Abstraction Interface Layer (FAIL) |
fansi |
0.4.0 | ANSI Control Sequence Aware String Functions |
fastcluster |
1.1.25 | Fast Hierarchical Clustering Routines for R and 'Python' |
fastICA |
1.2-1 | FastICA Algorithms to Perform ICA and Projection Pursuit |
fastmatch |
1.1-0 | Fast match() function |
FDb.InfiniumMethylation.hg19 |
2.2.0 | Annotation package for Illumina Infinium DNA methylation probes |
fdrtool |
1.2.15 | Estimation of (Local) False Discovery Rates and Higher Criticism |
FEM |
3.12.0 | Identification of Functional Epigenetic Modules |
fields |
9.8-3 | Tools for Spatial Data |
fit.models |
0.5-14 | Compare Fitted Models |
flashClust |
1.01-2 | Implementation of optimal hierarchical clustering |
flexmix |
2.3-15 | Flexible Mixture Modeling |
forcats |
0.4.0 | Tools for Working with Categorical Variables (Factors) |
foreach |
1.4.4 | Provides Foreach Looping Construct for R |
foreign |
0.8-71 | Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ... |
formatR |
1.6 | Format R Code Automatically |
Formula |
1.2-3 | Extended Model Formulas |
fpc |
2.2-3 | Flexible Procedures for Clustering |
fs |
1.3.1 | Cross-Platform File System Operations Based on 'libuv' |
futile.logger |
1.4.3 | A Logging Utility for R |
futile.options |
1.0.1 | Futile Options Management |
future |
1.13.0 | Unified Parallel and Distributed Processing in R for Everyone |
gam |
1.16.1 | Generalized Additive Models |
gamlss |
5.1-4 | Generalised Additive Models for Location Scale and Shape |
gamlss.data |
5.1-4 | GAMLSS Data |
gamlss.dist |
5.1-4 | Distributions for Generalized Additive Models for Location Scale and Shape |
gamlss.mx |
4.3-5 | Fitting Mixture Distributions with GAMLSS |
gamlss.nl |
4.1-0 | Fitting non linear parametric GAMLSS models |
gcrma |
2.56.0 | Background Adjustment Using Sequence Information |
gdalUtils |
2.0.1.14 | Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities |
gdata |
2.18.0 | Various R Programming Tools for Data Manipulation |
gdtools |
0.1.8 | Utilities for Graphical Rendering |
genefilter |
1.66.0 | genefilter: methods for filtering genes from high-throughput experiments |
geneLenDataBase |
1.20.0 | Lengths of mRNA transcripts for a number of genomes |
GeneNet |
1.2.13 | Modeling and Inferring Gene Networks |
geneplotter |
1.62.0 | Graphics related functions for Bioconductor |
generics |
0.0.2 | Common S3 Generics not Provided by Base R Methods Related to Model Fitting |
genetics |
1.3.8.1.2 | Population Genetics |
GenomeGraphs |
1.44.0 | Plotting genomic information from Ensembl |
GenomeInfoDb |
1.20.0 | Utilities for manipulating chromosome names, including modifying them to follow a particular naming style |
GenomeInfoDbData |
1.2.1 | Species and taxonomy ID look up tables used by GenomeInfoDb |
genomeIntervals |
1.40.0 | Operations on genomic intervals |
GenomicAlignments |
1.20.1 | Representation and manipulation of short genomic alignments |
GenomicFeatures |
1.36.3 | Conveniently import and query gene models |
GenomicRanges |
1.36.0 | Representation and manipulation of genomic intervals |
GEOquery |
2.52.0 | Get data from NCBI Gene Expression Omnibus (GEO) |
GGally |
1.4.0 | Extension to 'ggplot2' |
ggplot2 |
3.2.0 | Create Elegant Data Visualisations Using the Grammar of Graphics |
ggrepel |
0.8.1 | Automatically Position Non-Overlapping Text Labels with 'ggplot2' |
ggridges |
0.5.1 | Ridgeline Plots in 'ggplot2' |
gh |
1.0.1 | 'GitHub' 'API' |
git2r |
0.25.2 | Provides Access to Git Repositories |
GJRM |
0.2 | Generalised Joint Regression Modelling |
glmnet |
2.0-18 | Lasso and Elastic-Net Regularized Generalized Linear Models |
globals |
0.12.4 | Identify Global Objects in R Expressions |
globaltest |
5.38.0 | Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing |
glue |
1.3.1 | Interpreted String Literals |
gmodels |
2.18.1 | Various R Programming Tools for Model Fitting |
gmp |
0.5-13.5 | Multiple Precision Arithmetic |
goseq |
1.36.0 | Gene Ontology analyser for RNA-seq and other length biased data |
GOstats |
2.50.0 | Tools for manipulating GO and microarrays |
gower |
0.2.1 | Gower's Distance |
gplots |
3.0.1.1 | Various R Programming Tools for Plotting Data |
graph |
1.62.0 | graph: A package to handle graph data structures |
graphics |
3.6.0 | The R Graphics Package |
grDevices |
3.6.0 | The R Graphics Devices and Support for Colours and Fonts |
grid |
3.6.0 | The Grid Graphics Package |
gridExtra |
2.3 | Miscellaneous Functions for "Grid" Graphics |
GSEABase |
1.46.0 | Gene set enrichment data structures and methods |
gsl |
2.1-6 | Wrapper for the Gnu Scientific Library |
gsmoothr |
0.1.7 | Smoothing tools |
gtable |
0.3.0 | Arrange 'Grobs' in Tables |
gtools |
3.8.1 | Various R Programming Tools |
Gviz |
1.28.0 | Plotting data and annotation information along genomic coordinates |
HAC |
1.0-5 | Estimation, Simulation and Visualization of Hierarchical Archimedean Copulae (HAC) |
haplo.stats |
1.7.9 | Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous |
haven |
2.1.0 | Import and Export 'SPSS', 'Stata' and 'SAS' Files |
HDF5Array |
1.12.1 | HDF5 backend for DelayedArray objects |
hexbin |
1.27.3 | Hexagonal Binning Routines |
HI |
0.4 | Simulation from distributions supported by nested hyperplanes |
highr |
0.8 | Syntax Highlighting for R Source Code |
Hmisc |
4.2-0 | Harrell Miscellaneous |
hms |
0.4.2 | Pretty Time of Day |
HotDeckImputation |
1.1.0 | Hot Deck Imputation Methods for Missing Data |
htmlTable |
1.13.1 | Advanced Tables for Markdown/HTML |
htmltools |
0.3.6 | Tools for HTML |
htmlwidgets |
1.3 | HTML Widgets for R |
httpuv |
1.5.1 | HTTP and WebSocket Server Library |
httr |
1.4.0 | Tools for Working with URLs and HTTP |
hwriter |
1.3.2 | HTML Writer - Outputs R objects in HTML format |
igraph |
1.2.4.1 | Network Analysis and Visualization |
IlluminaHumanMethylation450kanno.ilmn12.hg19 |
0.6.0 | Annotation for Illumina's 450k methylation arrays |
IlluminaHumanMethylationEPICanno.ilm10b2.hg19 |
0.6.0 | Annotation for Illumina's EPIC methylation arrays |
IlluminaHumanMethylationEPICanno.ilm10b4.hg19 |
0.6.0 | Annotation for Illumina's EPIC methylation arrays |
IlluminaHumanMethylationEPICmanifest |
0.3.0 | Manifest for Illumina's EPIC methylation arrays |
illuminaio |
0.26.0 | Parsing Illumina Microarray Output Files |
impute |
1.58.0 | impute: Imputation for microarray data |
ini |
0.3.1 | Read and Write '.ini' Files |
inline |
0.3.15 | Functions to Inline C, C++, Fortran Function Calls from R |
intervals |
0.15.1 | Tools for Working with Points and Intervals |
ipred |
0.9-9 | Improved Predictors |
IRanges |
2.18.1 | Foundation of integer range manipulation in Bioconductor |
ISOcodes |
2019.04.22 | Selected ISO Codes |
isva |
1.9 | Independent Surrogate Variable Analysis |
iterators |
1.0.10 | Provides Iterator Construct for R |
JADE |
2.0-1 | Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria |
jsonlite |
1.6 | A Robust, High Performance JSON Parser and Generator for R |
kdecopula |
0.9.2 | Kernel Smoothing for Bivariate Copula Densities |
kernlab |
0.9-27 | Kernel-Based Machine Learning Lab |
KernSmooth |
2.23-15 | Functions for Kernel Smoothing Supporting Wand & Jones (1995) |
knitr |
1.23 | A General-Purpose Package for Dynamic Report Generation in R |
kohonen |
3.0.8 | Supervised and Unsupervised Self-Organising Maps |
kpmt |
0.1.0 | Known Population Median Test |
labeling |
0.3 | Axis Labeling |
lambda.r |
1.2.3 | Modeling Data with Functional Programming |
later |
0.8.0 | Utilities for Delaying Function Execution |
lattice |
0.20-38 | Trellis Graphics for R |
latticeExtra |
0.6-28 | Extra Graphical Utilities Based on Lattice |
lava |
1.6.5 | Latent Variable Models |
lazyeval |
0.2.2 | Lazy (Non-Standard) Evaluation |
leafem |
0.0.1 | 'leaflet' Extensions for 'mapview' |
leaflet |
2.0.2 | Create Interactive Web Maps with the JavaScript 'Leaflet' Library |
leafpop |
0.0.1 | Include Tables, Images and Graphs in Leaflet Pop-Ups |
leaps |
3.0 | Regression Subset Selection |
LearnBayes |
2.15.1 | Functions for Learning Bayesian Inference |
limma |
3.40.2 | Linear Models for Microarray Data |
listenv |
0.7.0 | Environments Behaving (Almost) as Lists |
lme4 |
1.1-21 | Linear Mixed-Effects Models using 'Eigen' and S4 |
lmtest |
0.9-37 | Testing Linear Regression Models |
locfit |
1.5-9.1 | Local Regression, Likelihood and Density Estimation. |
longitudinal |
1.1.12 | Analysis of Multiple Time Course Data |
loo |
2.1.0 | Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models |
lpSolve |
5.6.13.1 | Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs |
LSD |
4.0-0 | Lots of Superior Depictions |
ltm |
1.1-1 | Latent Trait Models under IRT |
lubridate |
1.7.4 | Make Dealing with Dates a Little Easier |
lumi |
2.36.0 | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
lwgeom |
0.1-7 | Bindings to Selected 'liblwgeom' Functions for Simple Features |
made4 |
1.58.0 | Multivariate analysis of microarray data using ADE4 |
magic |
1.5-9 | Create and Investigate Magic Squares |
magrittr |
1.5 | A Forward-Pipe Operator for R |
manipulateWidget |
0.10.0 | Add Even More Interactivity to Interactive Charts |
maps |
3.3.0 | Draw Geographical Maps |
maptools |
0.9-5 | Tools for Handling Spatial Objects |
maptree |
1.4-7 | Mapping, pruning, and graphing tree models |
mapview |
2.7.0 | Interactive Viewing of Spatial Data in R |
markdown |
0.9 | 'Markdown' Rendering for R |
marray |
1.62.0 | Exploratory analysis for two-color spotted microarray data |
MASS |
7.3-51.4 | Support Functions and Datasets for Venables and Ripley's MASS |
Matrix |
1.2-17 | Sparse and Dense Matrix Classes and Methods |
matrixcalc |
1.0-3 | Collection of functions for matrix calculations |
MatrixModels |
0.4-1 | Modelling with Sparse And Dense Matrices |
matrixStats |
0.54.0 | Functions that Apply to Rows and Columns of Matrices (and to Vectors) |
mclust |
5.4.4 | Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation |
mcmc |
0.9-6 | Markov Chain Monte Carlo |
memoise |
1.1.0 | Memoisation of Functions |
metafor |
2.1-0 | Meta-Analysis Package for R |
methods |
3.6.0 | Formal Methods and Classes |
methylumi |
2.30.0 | Handle Illumina methylation data |
mgcv |
1.8-28 | Mixed GAM Computation Vehicle with Automatic Smoothness Estimation |
mime |
0.6 | Map Filenames to MIME Types |
minfi |
1.30.0 | Analyze Illumina Infinium DNA methylation arrays |
miniUI |
0.1.1.1 | Shiny UI Widgets for Small Screens |
minqa |
1.2.4 | Derivative-free optimization algorithms by quadratic approximation |
missMethyl |
1.18.0 | Analysing Illumina HumanMethylation BeadChip Data |
mitools |
2.4 | Tools for Multiple Imputation of Missing Data |
mlr |
2.14.0 | Machine Learning in R |
mnormt |
1.5-5 | The Multivariate Normal and t Distributions |
ModelMetrics |
1.2.2 | Rapid Calculation of Model Metrics |
modelr |
0.1.4 | Modelling Functions that Work with the Pipe |
modeltools |
0.2-22 | Tools and Classes for Statistical Models |
msm |
1.6.7 | Multi-State Markov and Hidden Markov Models in Continuous Time |
mstate |
0.2.11 | Data Preparation, Estimation and Prediction in Multi-State Models |
multcomp |
1.4-10 | Simultaneous Inference in General Parametric Models |
multtest |
2.40.0 | Resampling-based multiple hypothesis testing |
munsell |
0.5.0 | Utilities for Using Munsell Colours |
mvtnorm |
1.0-11 | Multivariate Normal and t Distributions |
network |
1.15 | Classes for Relational Data |
nleqslv |
3.3.2 | Solve Systems of Nonlinear Equations |
nlme |
3.1-139 | Linear and Nonlinear Mixed Effects Models |
nloptr |
1.2.1 | R Interface to NLopt |
NLP |
0.2-0 | Natural Language Processing Infrastructure |
nnet |
7.3-12 | Feed-Forward Neural Networks and Multinomial Log-Linear Models |
nor1mix |
1.3-0 | Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods) |
numDeriv |
2016.8-1.1 | Accurate Numerical Derivatives |
nutshell |
2.0 | Data for "R in a Nutshell" |
nutshell.audioscrobbler |
1.0 | Audioscrobbler data for "R in a Nutshell" |
nutshell.bbdb |
1.0 | Baseball Database for "R in a Nutshell" |
OPE |
0.7 | Outer-product emulator |
openssl |
1.4 | Toolkit for Encryption, Signatures and Certificates Based on OpenSSL |
openxlsx |
4.1.0.1 | Read, Write and Edit XLSX Files |
packrat |
0.5.0 | A Dependency Management System for Projects and their R Package Dependencies |
panelAR |
0.1 | Estimation of Linear AR(1) Panel Data Models with Cross-Sectional Heteroskedasticity and/or Correlation |
parallel |
3.6.0 | Support for Parallel computation in R |
parallelMap |
1.4 | Unified Interface to Parallelization Back-Ends |
ParamHelpers |
1.12 | Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning |
parcor |
0.2-6 | Regularized estimation of partial correlation matrices |
pbkrtest |
0.4-7 | Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison |
pcaPP |
1.9-73 | Robust PCA by Projection Pursuit |
pegas |
0.11 | Population and Evolutionary Genetics Analysis System |
permute |
0.9-5 | Functions for Generating Restricted Permutations of Data |
phangorn |
2.5.5 | Phylogenetic Reconstruction and Analysis |
pillar |
1.4.1 | Coloured Formatting for Columns |
pixmap |
0.4-11 | Bitmap Images (``Pixel Maps'') |
pkgbuild |
1.0.3 | Find Tools Needed to Build R Packages |
pkgconfig |
2.0.2 | Private Configuration for 'R' Packages |
pkgload |
1.0.2 | Simulate Package Installation and Attach |
pkgmaker |
0.27 | Development Utilities for R Packages |
plogr |
0.2.0 | The 'plog' C++ Logging Library |
plotly |
4.9.0 | Create Interactive Web Graphics via 'plotly.js' |
pls |
2.7-1 | Partial Least Squares and Principal Component Regression |
plyr |
1.8.4 | Tools for Splitting, Applying and Combining Data |
png |
0.1-7 | Read and write PNG images |
poLCA |
1.4.1 | Polytomous variable Latent Class Analysis |
polspline |
1.1.14 | Polynomial Spline Routines |
polycor |
0.7-9 | Polychoric and Polyserial Correlations |
poweRlaw |
0.70.2 | Analysis of Heavy Tailed Distributions |
ppls |
1.6-1.1 | Penalized Partial Least Squares |
prabclus |
2.3-1 | Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data |
pracma |
2.2.5 | Practical Numerical Math Functions |
praise |
1.0.0 | Praise Users |
preprocessCore |
1.46.0 | A collection of pre-processing functions |
prettydoc |
0.2.1 | Creating Pretty Documents from R Markdown |
prettyunits |
1.0.2 | Pretty, Human Readable Formatting of Quantities |
processx |
3.3.1 | Execute and Control System Processes |
prodlim |
2018.04.18 | Product-Limit Estimation for Censored Event History Analysis |
progress |
1.2.2 | Terminal Progress Bars |
promises |
1.0.1 | Abstractions for Promise-Based Asynchronous Programming |
ProtGenerics |
1.16.0 | S4 generic functions for Bioconductor proteomics infrastructure |
proto |
1.0.0 | Prototype Object-Based Programming |
proxyC |
0.1.5 | Computes Proximity in Large Sparse Matrices |
ps |
1.3.0 | List, Query, Manipulate System Processes |
PSCBS |
0.65.0 | Analysis of Parent-Specific DNA Copy Numbers |
pspline |
1.0-18 | Penalized Smoothing Splines |
psych |
1.8.12 | Procedures for Psychological, Psychometric, and Personality Research |
purrr |
0.3.2 | Functional Programming Tools |
qrng |
0.0-5 | (Randomized) Quasi-Random Number Generators |
quadprog |
1.5-7 | Functions to Solve Quadratic Programming Problems |
quanteda |
1.5.1 | Quantitative Analysis of Textual Data |
quantmod |
0.4-14 | Quantitative Financial Modelling Framework |
quantreg |
5.41 | Quantile Regression |
qvalue |
2.16.0 | Q-value estimation for false discovery rate control |
R.cache |
0.13.0 | Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations |
R.devices |
2.16.0 | Unified Handling of Graphics Devices |
R.filesets |
2.13.0 | Easy Handling of and Access to Files Organized in Structured Directories |
R.huge |
0.9.0 | Methods for Accessing Huge Amounts of Data [deprecated] |
R.methodsS3 |
1.7.1 | S3 Methods Simplified |
R.oo |
1.22.0 | R Object-Oriented Programming with or without References |
R.rsp |
0.43.1 | Dynamic Generation of Scientific Reports |
R.utils |
2.9.0 | Various Programming Utilities |
R2HTML |
2.3.2 | HTML Exportation for R Objects |
R2jags |
0.5-7 | Using R to Run 'JAGS' |
R2WinBUGS |
2.1-21 | Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS' |
R6 |
2.4.0 | Encapsulated Classes with Reference Semantics |
randomForest |
4.6-14 | Breiman and Cutler's Random Forests for Classification and Regression |
rappdirs |
0.3.1 | Application Directories: Determine Where to Save Data, Caches, and Logs |
raster |
2.9-5 | Geographic Data Analysis and Modeling |
RBGL |
1.60.0 | An interface to the BOOST graph library |
rcmdcheck |
1.3.3 | Run 'R CMD check' from 'R' and Capture Results |
RColorBrewer |
1.1-2 | ColorBrewer Palettes |
Rcpp |
1.0.1 | Seamless R and C++ Integration |
RcppArmadillo |
0.9.500.2.0 | 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library |
RcppEigen |
0.3.3.5.0 | 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library |
RcppGSL |
0.3.6 | 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices |
RcppParallel |
4.4.3 | Parallel Programming Tools for 'Rcpp' |
RcppRoll |
0.3.0 | Efficient Rolling / Windowed Operations |
RCurl |
1.95-4.12 | General Network (HTTP/FTP/...) Client Interface for R |
readr |
1.3.1 | Read Rectangular Text Data |
readxl |
1.3.1 | Read Excel Files |
recipes |
0.1.5 | Preprocessing Tools to Create Design Matrices |
registry |
0.5-1 | Infrastructure for R Package Registries |
relaimpo |
2.2-3 | Relative Importance of Regressors in Linear Models |
rematch |
1.0.1 | Match Regular Expressions with a Nicer 'API' |
remotes |
2.0.4 | R Package Installation from Remote Repositories, Including 'GitHub' |
Repitools |
1.30.0 | Epigenomic tools |
reprex |
0.3.0 | Prepare Reproducible Example Code via the Clipboard |
reshape |
0.8.8 | Flexibly Reshape Data |
reshape2 |
1.4.3 | Flexibly Reshape Data: A Reboot of the Reshape Package |
reticulate |
1.13 | Interface to 'Python' |
rgdal |
1.4-4 | Bindings for the 'Geospatial' Data Abstraction Library |
rgeos |
0.4-3 | Interface to Geometry Engine - Open Source ('GEOS') |
rgl |
0.100.24 | 3D Visualization Using OpenGL |
Rglpk |
0.6-4 | R/GNU Linear Programming Kit Interface |
Rgraphviz |
2.28.0 | Provides plotting capabilities for R graph objects |
rhdf5 |
2.28.0 | R Interface to HDF5 |
Rhdf5lib |
1.6.0 | hdf5 library as an R package |
Rhtslib |
1.16.1 | HTSlib high-throughput sequencing library as an R package |
Ringo |
1.48.0 | R Investigation of ChIP-chip Oligoarrays |
rio |
0.5.16 | A Swiss-Army Knife for Data I/O |
rjags |
4-8 | Bayesian Graphical Models using MCMC |
RJSONIO |
1.3-1.2 | Serialize R Objects to JSON, JavaScript Object Notation |
rlang |
0.3.4 | Functions for Base Types and Core R and 'Tidyverse' Features |
rlecuyer |
0.3-4 | R Interface to RNG with Multiple Streams |
rlist |
0.4.6.1 | A Toolbox for Non-Tabular Data Manipulation |
rmarkdown |
1.13 | Dynamic Documents for R |
Rmpfr |
0.7-2 | R MPFR - Multiple Precision Floating-Point Reliable |
Rmpi |
0.6-9 | Interface (Wrapper) to MPI (Message-Passing Interface) |
rms |
5.1-3.1 | Regression Modeling Strategies |
RMySQL |
0.10.17 | Database Interface and 'MySQL' Driver for R |
RNetCDF |
1.9-1 | Interface to NetCDF Datasets |
rngtools |
1.4 | Utility Functions for Working with Random Number Generators |
robust |
0.4-18 | Port of the S+ "Robust Library" |
robustbase |
0.93-5 | Basic Robust Statistics |
ROC |
1.60.0 | utilities for ROC, with uarray focus |
rpart |
4.1-15 | Recursive Partitioning and Regression Trees |
RPMM |
1.25 | Recursively Partitioned Mixture Model |
rprojroot |
1.3-2 | Finding Files in Project Subdirectories |
rrcov |
1.4-7 | Scalable Robust Estimators with High Breakdown Point |
Rsamtools |
2.0.0 | Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import |
rsconnect |
0.8.13 | Deployment Interface for R Markdown Documents and Shiny Applications |
Rsolnp |
1.16 | General Non-Linear Optimization |
RSpectra |
0.15-0 | Solvers for Large-Scale Eigenvalue and SVD Problems |
RSQLite |
2.1.1 | 'SQLite' Interface for R |
rstan |
2.18.2 | R Interface to Stan |
rstanarm |
2.18.2 | Bayesian Applied Regression Modeling via Stan |
rstantools |
1.5.1 | Tools for Developing R Packages Interfacing with 'Stan' |
rstudioapi |
0.10 | Safely Access the RStudio API |
Rsubread |
1.34.4 | Subread Sequence Alignment and Counting for R |
rtracklayer |
1.44.0 | R interface to genome annotation files and the UCSC genome browser |
Rttf2pt1 |
1.3.7 | 'ttf2pt1' Program |
ruv |
0.9.7 | Detect and Remove Unwanted Variation using Negative Controls |
rvest |
0.3.4 | Easily Harvest (Scrape) Web Pages |
S4Vectors |
0.22.0 | Foundation of vector-like and list-like containers in Bioconductor |
saemix |
2.2 | Stochastic Approximation Expectation Maximization (SAEM) Algorithm |
sampling |
2.8 | Survey Sampling |
sandwich |
2.5-1 | Robust Covariance Matrix Estimators |
satellite |
1.0.1 | Handling and Manipulating Remote Sensing Data |
scales |
1.0.0 | Scale Functions for Visualization |
scam |
1.2-4 | Shape Constrained Additive Models |
scatterplot3d |
0.3-41 | 3D Scatter Plot |
schoolmath |
0.4 | Functions and datasets for math used in school |
scrime |
1.3.5 | Analysis of High-Dimensional Categorical Data Such as SNP Data |
segmented |
0.5-4.0 | Regression Models with Break-Points / Change-Points Estimation |
selectr |
0.4-1 | Translate CSS Selectors to XPath Expressions |
sendmailR |
1.2-1 | send email using R |
seqinr |
3.4-5 | Biological Sequences Retrieval and Analysis |
seqLogo |
1.50.0 | Sequence logos for DNA sequence alignments |
sessioninfo |
1.1.1 | R Session Information |
sf |
0.7-4 | Simple Features for R |
sfsmisc |
1.1-4 | Utilities from 'Seminar fuer Statistik' ETH Zurich |
shiny |
1.3.2 | Web Application Framework for R |
shinyjs |
1.0 | Easily Improve the User Experience of Your Shiny Apps in Seconds |
shinystan |
2.5.0 | Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models |
shinythemes |
1.1.2 | Themes for Shiny |
ShortRead |
1.42.0 | FASTQ input and manipulation |
siggenes |
1.58.0 | Multiple Testing using SAM and Efron's Empirical Bayes Approaches |
simpleaffy |
2.60.0 | Very simple high level analysis of Affymetrix data |
slam |
0.1-45 | Sparse Lightweight Arrays and Matrices |
sn |
1.5-4 | The Skew-Normal and Related Distributions Such as the Skew-t |
sna |
2.4 | Tools for Social Network Analysis |
snow |
0.4-3 | Simple Network of Workstations |
SnowballC |
0.6.0 | Snowball Stemmers Based on the C 'libstemmer' UTF-8 Library |
snowfall |
1.84-6.1 | Easier cluster computing (based on snow). |
softImpute |
1.4 | Matrix Completion via Iterative Soft-Thresholded SVD |
sourcetools |
0.1.7 | Tools for Reading, Tokenizing and Parsing R Code |
sp |
1.3-1 | Classes and Methods for Spatial Data |
spacyr |
1.2 | Wrapper to the 'spaCy' 'NLP' Library |
spam |
2.2-2 | SPArse Matrix |
SparseM |
1.77 | Sparse Linear Algebra |
spatial |
7.3-11 | Functions for Kriging and Point Pattern Analysis |
spData |
0.3.0 | Datasets for Spatial Analysis |
spdep |
1.1-2 | Spatial Dependence: Weighting Schemes, Statistics and Models |
splines |
3.6.0 | Regression Spline Functions and Classes |
SQUAREM |
2017.10-1 | Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms |
stabledist |
0.7-1 | Stable Distribution Functions |
StanHeaders |
2.18.1 | C++ Header Files for Stan |
startupmsg |
0.9.6 | Utilities for Start-Up Messages |
statmod |
1.4.32 | Statistical Modeling |
statnet.common |
4.3.0 | Common R Scripts and Utilities Used by the Statnet Project Software |
stats |
3.6.0 | The R Stats Package |
stats4 |
3.6.0 | Statistical Functions using S4 Classes |
stopwords |
1.0 | Multilingual Stopword Lists |
stringdist |
0.9.5.2 | Approximate String Matching and String Distance Functions |
stringi |
1.4.3 | Character String Processing Facilities |
stringr |
1.4.0 | Simple, Consistent Wrappers for Common String Operations |
SummarizedExperiment |
1.14.0 | SummarizedExperiment container |
survey |
3.36 | Analysis of Complex Survey Samples |
survival |
2.44-1.1 | Survival Analysis |
sva |
3.32.1 | Surrogate Variable Analysis |
svglite |
1.2.2 | An 'SVG' Graphics Device |
sys |
3.2 | Powerful and Reliable Tools for Running System Commands in R |
systemfit |
1.1-22 | Estimating Systems of Simultaneous Equations |
TAM |
3.2-24 | Test Analysis Modules |
tcltk |
3.6.0 | Tcl/Tk Interface |
testthat |
2.1.1 | Unit Testing for R |
tgp |
2.4-14 | Bayesian Treed Gaussian Process Models |
TH.data |
1.0-10 | TH's Data Archive |
threejs |
0.3.1 | Interactive 3D Scatter Plots, Networks and Globes |
tibble |
2.1.2 | Simple Data Frames |
tidyr |
0.8.3 | Easily Tidy Data with 'spread()' and 'gather()' Functions |
tidyselect |
0.2.5 | Select from a Set of Strings |
tidyverse |
1.2.1 | Easily Install and Load the 'Tidyverse' |
timeDate |
3043.102 | Rmetrics - Chronological and Calendar Objects |
tinytex |
0.13 | Helper Functions to Install and Maintain 'TeX Live', and Compile 'LaTeX' Documents |
tkrplot |
0.0-24 | TK Rplot |
tm |
0.7-6 | Text Mining Package |
tmap |
2.2 | Thematic Maps |
tmaptools |
2.0-1 | Thematic Map Tools |
tools |
3.6.0 | Tools for Package Development |
topicmodels |
0.2-8 | Topic Models |
truncnorm |
1.0-8 | Truncated Normal Distribution |
trust |
0.1-7 | Trust Region Optimization |
trustOptim |
0.8.6.2 | Trust Region Optimization for Nonlinear Functions with Sparse Hessians |
tseries |
0.10-47 | Time Series Analysis and Computational Finance |
TTR |
0.23-4 | Technical Trading Rules |
TxDb.Hsapiens.UCSC.hg19.knownGene |
3.2.2 | Annotation package for TxDb object(s) |
udunits2 |
0.13 | Udunits-2 Bindings for R |
units |
0.6-3 | Measurement Units for R Vectors |
urca |
1.3-0 | Unit Root and Cointegration Tests for Time Series Data |
usethis |
1.5.0 | Automate Package and Project Setup |
utf8 |
1.1.4 | Unicode Text Processing |
utils |
3.6.0 | The R Utils Package |
uuid |
0.1-2 | Tools for generating and handling of UUIDs |
V8 |
2.3 | Embedded JavaScript Engine for R |
VariantAnnotation |
1.30.1 | Annotation of Genetic Variants |
vctrs |
0.1.0 | Vector Helpers |
vegan |
2.5-5 | Community Ecology Package |
VGAM |
1.1-1 | Vector Generalized Linear and Additive Models |
VineCopula |
2.1.8 | Statistical Inference of Vine Copulas |
viridis |
0.5.1 | Default Color Maps from 'matplotlib' |
viridisLite |
0.3.0 | Default Color Maps from 'matplotlib' (Lite Version) |
vsn |
3.52.0 | Variance stabilization and calibration for microarray data |
wateRmelon |
1.28.0 | Illumina 450 methylation array normalization and metrics |
webshot |
0.5.1 | Take Screenshots of Web Pages |
WGCNA |
1.68 | Weighted Correlation Network Analysis |
whisker |
0.3-2 | {{mustache}} for R, logicless templating |
widgetTools |
1.62.0 | Creates an interactive tcltk widget |
withr |
2.1.2 | Run Code 'With' Temporarily Modified Global State |
xfun |
0.7 | Miscellaneous Functions by 'Yihui Xie' |
XML |
3.98-1.20 | Tools for Parsing and Generating XML Within R and S-Plus |
xml2 |
1.2.0 | Parse XML |
xopen |
1.0.0 | Open System Files, 'URLs', Anything |
xps |
1.44.0 | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |
xtable |
1.8-4 | Export Tables to LaTeX or HTML |
xts |
0.11-2 | eXtensible Time Series |
XVector |
0.24.0 | Foundation of external vector representation and manipulation in Bioconductor |
yaml |
2.2.0 | Methods to Convert R Data to YAML and Back |
zeallot |
0.1.0 | Multiple, Unpacking, and Destructuring Assignment |
zip |
2.0.2 | Cross-Platform 'zip' Compression |
zlibbioc |
1.30.0 | An R packaged zlib-1.2.5 |
zoo |
1.8-6 | S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations) |