R is a free software environment for statistical computing and graphics.
...
R packages are built using SPACK optimized for the underlying CPU architecture or binary installs using Conda. Applications built by RC staff that are dependent on R use the SPACK built R packages.
| Info |
|---|
The conda/spark module was built for use with Apache Spark and provides Python packages such as pyspark |
| Expand |
|---|
| title | Package List (as of Dec 10, 2021) |
|---|
|
Package | 4.0.3 SPACK | 4.0.5 Conda | 4.1.1 SPARK |
|---|
abind |
| 1.4-5 | 1.4-5 | acepack | 1.4.1 |
|
| amap | 0.8-17 |
|
| animation | 2.6 |
|
| annotate | 1.62.0 |
|
| AnnotationDbi | 1.46.1 |
|
| ape | 5.3 |
|
| argparse | 2.0.1 |
|
| askpass | 1.1 | 1.1 | 1.1 | assertthat | 0.2.1 | 0.2.1 | 0.2.1 | backports | 1.1.4 | 1.4.0 | 1.4.0 | base | 4.0.3 | 4.0.5 | 4.1.1 | base64enc | 0.1-3 | 0.1-3 | 0.1-3 | BBmisc | 1.11 |
|
| BH | 1.69.0-1 |
|
| BiasedUrn | 1.07 |
|
| bibtex | 0.4.2 |
|
| bigmemory | 4.5.36 |
|
| bigmemory.sri | 0.1.3 |
|
| Biobase | 2.44.0 |
|
| BiocGenerics | 0.34.0 |
|
| BiocManager | 1.30.10 | 1.30.16 | 1.30.16 | BiocParallel | 1.18.1 |
|
| BiocVersion |
|
| 3.14.0 | biomaRt | 2.40.5 |
|
| Biostrings | 2.52.0 |
|
| bit | 1.1-14 | 4.0.4 | 4.0.4 | bit64 | 0.9-7 | 4.0.5 | 4.0.5 | bitops | 1.0-6 | 1.0-7 | 1.0-7 | blob | 1.2.0 | 1.2.2 | 1.2.2 | boot | 1.3-27 | 1.3-28 | 1.3-28 | brew | 1.0-6 |
|
| brio |
| 1.1.3 | 1.1.3 | broom | 0.5.2 | 0.7.10 | 0.7.10 | bslib |
| 0.3.1 | 0.3.1 | cachem |
| 1.0.6 | 1.0.6 | callr | 3.4.3 | 3.7.0 | 3.7.0 | car |
| 3.0-12 | 3.0-12 | carData |
| 3.0-4 | 3.0-4 | caret | 6.0-84 | 6.0-90 | 6.0-90 | caTools | 1.17.1.2 |
|
| cellranger | 1.1.0 | 1.1.0 | 1.1.0 | checkmate | 1.9.4 |
|
| chron | 2.3-53 |
|
| class | 7.3-18 | 7.3-19 | 7.3-19 | cli | 2.0.2 | 3.1.0 | 3.1.0 | clipr | 0.7.0 | 0.7.1 | 0.7.1 | cluster | 2.1.1 | 2.1.2 | 2.1.2 | clusterGeneration | 1.3.4 |
|
| coda | 0.19-3 |
|
| codetools | 0.2-18 | 0.2-18 | 0.2-18 | colorspace | 1.4-1 | 2.0-2 | 2.0-2 | combinat | 0.0-8 |
|
| commonmark | 1.7 | 1.7 | 1.7 | compiler | 4.0.3 | 4.0.5 | 4.1.1 | config |
| 0.3.1 | 0.3.1 | conquer |
| 1.2.1 | 1.2.1 | corrplot |
| 0.92 | 0.92 | covr | 3.5.0 |
|
| cowplot | 1.0.0 | 1.1.1 | 1.1.1 | cpp11 |
| 0.4.2 | 0.4.2 | crayon | 1.3.4 | 1.4.2 | 1.4.2 | crosstalk | 1.0.0 | 1.2.0 | 1.2.0 | crul |
| 1.2.0 | 1.2.0 | ctc | 1.58.0 |
|
| curl | 4.3 | 4.3.2 | 4.3.2 | data.table | 1.12.8 | 1.14.2 | 1.14.2 | datasets | 4.0.3 | 4.0.5 | 4.1.1 | DBI | 1.1.0 | 1.1.1 | 1.1.1 | dbplyr | 1.4.2 | 2.1.1 | 2.1.1 | DelayedArray | 0.10.0 |
|
| dendextend | 1.12.0 |
|
| desc | 1.2.0 | 1.4.0 | 1.4.0 | DESeq2 | 1.24.0 |
|
| devtools | 2.3.0 |
|
| DEXSeq | 1.36.0 |
|
| DiagrammeR |
| 1.0.6.1 | 1.0.6.1 | diffobj |
| 0.3.5 | 0.3.5 | digest | 0.6.25 | 0.6.29 | 0.6.29 | doParallel | 1.0.15 |
|
| downloader |
| 0.4 | 0.4 | dplyr | 0.8.3 | 1.0.7 | 1.0.7 | dqrng | 0.2.1 |
|
| DT | 0.13 | 0.20 | 0.20 | dtplyr |
| 1.2.0 | 1.2.0 | dygraphs | 1.1.1.6 | 1.1.1.6 | 1.1.1.6 | e1071 |
| 1.7-9 | 1.7-9 | edgeR | 3.26.8 |
|
| ellipsis | 0.3.0 | 0.3.2 | 0.3.2 | evaluate | 0.14 | 0.14 | 0.14 | expm | 0.999-4 |
|
| fansi | 0.4.0 | 0.5.0 | 0.4.2 | farver |
| 2.1.0 | 2.1.0 | fastcluster | 1.1.25 |
|
| fastmap |
| 1.1.0 | 1.1.0 | fastmatch | 1.1-0 |
|
| findpython | 1.0.5 |
|
| fitdistrplus | 1.0-14 |
|
| flexdashboard |
| 0.5.2 | 0.5.2 | FNN | 1.1.3 |
|
| fontawesome |
| 0.2.2 | 0.2.2 | forcats | 0.4.0 | 0.5.1 | 0.5.1 | foreach | 1.4.7 | 1.5.1 | 1.5.1 | foreign | 0.8-81 | 0.8-81 | 0.8-81 | forge |
| 0.2.0 | 0.2.0 | formatR | 1.7 | 1.11 | 1.11 | Formula | 1.2-3 |
|
| fs | 1.3.1 | 1.5.2 | 1.5.2 | futile.logger | 1.4.3 |
|
| futile.options | 1.0.1 |
|
| future | 1.14.0 | 1.23.0 | 1.23.0 | future.apply | 1.3.0 | 1.8.1 | 1.8.1 | gapminder |
| 0.3.0 | 0.3.0 | gargle |
| 1.2.0 | 1.2.0 | gbRd | 0.4-11 |
|
| gdata | 2.18.0 |
|
| gdtools |
| 0.2.3 | 0.2.3 | genefilter | 1.72.1 |
|
| geneLenDataBase | 1.20.0 |
|
| geneplotter | 1.62.0 |
|
| generics | 0.0.2 | 0.1.1 | 0.1.1 | GenomeInfoDb | 1.20.0 |
|
| GenomeInfoDbData | 1.2.1 |
|
| GenomicAlignments | 1.20.1 |
|
| GenomicFeatures | 1.36.4 |
|
| GenomicRanges | 1.36.1 |
|
| gganimate |
| 1.0.7 | 1.0.7 | ggdendro | 0.1-20 |
|
| ggplot2 | 3.2.0 | 3.3.5 | 3.3.5 | ggpubr |
| 0.4.0 | 0.4.0 | ggrepel | 0.8.1 | 0.9.1 | 0.9.1 | ggridges | 0.5.1 |
|
| ggsci |
| 2.9 | 2.9 | ggsignif |
| 0.6.3 | 0.6.3 | ggthemes |
| 4.2.4 | 4.2.4 | ggvis |
| 0.4.7 | 0.4.7 | gh | 1.1.0 |
|
| gistr | 0.4.2 | 0.9.0 | 0.9.0 | git2r | 0.27.1 |
|
| Glimma | 1.12.0 |
|
| glmnet |
| 4.1-2 | 4.1-2 | globals | 0.12.4 | 0.14.0 | 0.14.0 | glue | 1.4.1 | 1.5.1 | 1.5.1 | gmodels | 2.18.1 |
|
| GO.db | 3.4.1 |
|
| googleAuthR |
|
| 1.4.0 | googledrive |
| 2.0.0 | 2.0.0 | googlesheets4 |
| 1.0.0 | 1.0.0 | googleVis |
| 0.6.10 | 0.6.10 | GOplot | 1.0.2 |
|
| goseq | 1.36.0 |
|
| gower | 0.2.1 | 0.2.2 | 0.2.2 | gplots | 3.0.1.1 |
|
| graphics | 4.0.3 | 4.0.5 | 4.1.1 | grDevices | 4.0.3 | 4.0.5 | 4.1.1 | grid | 4.0.3 | 4.0.5 | 4.1.1 | gridExtra | 2.3 | 2.3 | 2.3 | gsubfn | 0.7 |
|
| gtable | 0.3.0 | 0.3.0 | 0.3.0 | gtools | 3.8.1 |
|
| haven | 2.1.1 | 2.4.3 | 2.4.3 | hdf5r | 1.2.0 |
|
| here |
| 1.0.1 | 1.0.1 | hexbin | 1.27.3 | 1.28.2 | 1.28.2 | highr | 0.8 | 0.9 | 0.9 | Hmisc | 4.4-0 |
|
| hms | 0.5.0 | 1.1.1 | 1.1.1 | htmlTable | 1.13.1 |
|
| htmltools | 0.3.6 | 0.5.2 | 0.5.2 | htmlwidgets | 1.3 | 1.5.4 | 1.5.4 | httpcode |
| 0.3.0 | 0.3.0 | httpuv | 1.5.1 | 1.6.3 | 1.6.3 | httr | 1.4.1 | 1.4.2 | 1.4.2 | hwriter | 1.3.2 |
|
| ica | 1.0-2 |
|
| ids |
| 1.0.1 | 1.0.1 | igraph | 1.2.4.1 | 1.2.6 | 1.2.9 | influenceR |
| 0.1.0.1 | 0.1.0.1 | ini | 0.3.1 |
|
| inline | 0.3.15 |
|
| ipred | 0.9-9 | 0.9-12 | 0.9-12 | IRanges | 2.22.2 |
|
| IRdisplay |
| 1.0 | 1.0 | IRkernel |
| 1.2 | 1.2 | irlba | 2.3.3 |
|
| isoband |
| 0.2.5 | 0.2.5 | iterators | 1.0.12 | 1.0.13 | 1.0.13 | janitor | 1.2.0 |
|
| jquerylib |
| 0.1.4 | 0.1.4 | jsonlite | 1.6.1 | 1.7.2 | 1.7.2 | kableExtra |
| 1.3.4 | 1.3.4 | KernSmooth | 2.23-18 | 2.23-20 | 2.23-20 | knitr | 1.28 | 1.36 | 1.35 | labeling | 0.3 | 0.4.2 | 0.4.2 | Lahman |
| 9.0-0 | 9.0-0 | lambda.r | 1.2.3 |
|
| later | 0.8.0 | 1.2.0 | 1.2.0 | lattice | 0.20-41 | 0.20-45 | 0.20-45 | latticeExtra | 0.6-28 |
|
| lava | 1.6.6 | 1.6.10 | 1.6.10 | lazyeval | 0.2.2 | 0.2.2 | 0.2.2 | leaflet |
| 2.0.4.1 | 2.0.4.1 | leaflet.providers |
| 1.9.0 | 1.9.0 | leiden | 0.3.1 |
|
| lifecycle |
| 1.0.1 | 1.0.1 | limma | 3.40.6 |
|
| listenv | 0.7.0 | 0.8.0 | 0.8.0 | lme4 | 1.1-21 | 1.1-27.1 | 1.1-27.1 | lmtest | 0.9-37 |
|
| lobstr |
| 1.1.1 | 1.1.1 | locfit | 1.5-9.1 |
|
| loo | 2.1.0 |
|
| lsei | 1.2-0 |
|
| lubridate | 1.7.4 | 1.8.0 | 1.8.0 | magick | 2.1 | 2.7.3 | 2.7.3 | magrittr | 1.5 | 2.0.1 | 2.0.1 | maps | 3.3.0 | 3.4.0 | 3.4.0 | maptools |
| 1.1-2 | 1.1-2 | markdown | 1.1 | 1.1 | 1.1 | MASS | 7.3-53.1 | 7.3-54 | 7.3-54 | Matrix | 1.3-2 | 1.3-4 | 1.3-4 | MatrixModels |
| 0.5-0 | 0.5-0 | matrixStats | 0.55.0 | 0.61.0 | 0.61.0 | memoise | 1.1.0 |
| 2.0.1 | metap | 1.1 |
|
| methods | 4.0.3 | 4.0.5 | 4.1.1 | mgcv | 1.8-34 | 1.8-38 | 1.8-38 | mime | 0.7 | 0.12 | 0.12 | minqa | 1.2.4 | 1.2.4 | 1.2.4 | mlr | 2.15.0 |
|
| mnormt | 1.5-5 |
|
| ModelMetrics | 1.2.2 | 1.2.2.2 | 1.2.2.2 | modelr | 0.1.5 | 0.1.8 | 0.1.8 | multtest | 2.40.0 |
|
| munsell | 0.5.0 | 0.5.0 | 0.5.0 | ncdf4 | 1.16.1 |
|
| nlme | 3.1-152 | 3.1-150 | 3.1-153 | nloptr | 1.2.1 | 1.2.2.2 | 1.2.2.3 | nnet | 7.3-15 | 7.3-16 | 7.3-16 | npsurv | 0.4-0 |
|
| numDeriv | 2016.8-1.1 | 2016.8-1.1 | 2016.8-1.1 | nycflights13 |
| 1.0.2 | 1.0.2 | openssl | 1.4.1 | 1.4.5 | 1.4.5 | openxlsx | 4.1.0.1 | 4.2.4 | 4.2.4 | pacman | 0.5.1 | 0.5.1 | 0.5.1 | parallel | 4.0.3 | 4.0.5 | 4.1.1 | parallelly |
| 1.29.0 | 1.29.0 | parallelMap | 1.4 |
|
| ParamHelpers | 1.12 |
|
| pbapply | 1.4-1 |
|
| pbdZMQ |
| 0.3-6 | 0.3-6 | pbkrtest |
| 0.5.1 | 0.5.1 | pdftools |
| 3.0.1 | 3.0.1 | phangorn | 2.5.5 |
|
| phytools | 0.6-99 |
|
| pillar | 1.4.2 | 1.6.4 | 1.6.4 | pkgbuild | 1.0.8 |
|
| pkgconfig | 2.0.2 | 2.0.3 | 2.0.3 | pkgload | 1.0.2 | 1.2.4 | 1.2.4 | plogr | 0.2.0 |
|
| plotly | 4.9.0 | 4.10.0 | 4.10.0 | plotrix | 3.7-6 |
|
| plyr | 1.8.4 | 1.8.6 | 1.8.6 | png | 0.1-7 | 0.1-7 | 0.1-7 | polynom |
| 1.4-0 | 1.4-0 | praise | 1.0.0 | 1.0.0 | 1.0.0 | prettyunits | 1.0.2 | 1.1.1 | 1.1.1 | pROC |
| 1.18.0 | 1.18.0 | processx | 3.4.1 | 3.5.2 | 3.5.2 | prodlim | 2018.04.18 | 2019.11.13 | 2019.11.13 | progress | 1.2.2 | 1.2.2 | 1.2.2 | progressr |
| 0.9.0 | 0.9.0 | promises | 1.0.1 | 1.2.0.1 | 1.2.0.1 | proto | 1.0.0 |
|
| proxy |
| 0.4-26 | 0.4-26 | pryr | 0.1.4 | 0.1.5 | 0.1.5 | ps | 1.3.0 | 1.6.0 | 1.6.0 | purrr | 0.3.4 | 0.3.4 | 0.3.4 | qpdf |
| 1.1 | 1.1 | quadprog | 1.5-7 |
|
| quantmod | 0.4-15 | 0.4.18 | 0.4.18 | quantreg |
| 5.86 | 5.86 | qvalue | 2.16.0 |
|
| R.methodsS3 | 1.7.1 |
|
| R.oo | 1.23.0 |
|
| R.utils | 2.9.0 |
|
| r2d3 |
| 0.2.5 | 0.2.5 | R6 | 2.4.0 | 2.5.1 | 2.5.1 | randomForest | 4.6-14 | 4.6-14 | 4.6-14 | RANN | 2.6.1 |
|
| rappdirs | 0.3.1 | 0.3.3 | 0.3.3 | raster |
| 3.4-13 | 3.5-2 | rbokeh | 0.5.0 | 0.5.2 | 0.5.2 | rcmdcheck | 1.3.3 |
|
| RColorBrewer | 1.1-2 | 1.1-2 | 1.1-2 | Rcpp | 1.0.4.6 | 1.0.7 | 1.0.7 | RcppAnnoy | 0.0.12 |
|
| RcppArmadillo | 0.9.600.4.0 | 0.10.7.3.0 | 0.10.7.3.0 | RcppEigen | 0.3.3.5.0 | 0.3.3.9.1 | 0.3.3.9.1 | RcppParallel | 4.4.3 |
|
| RcppProgress | 0.4.1 |
|
| RCurl | 1.98-1.2 | 1.98-1.5 | 1.98-1.5 | Rdpack | 0.11-0 |
|
| readr | 1.3.1 | 2.1.1 | 2.1.1 | readxl | 1.3.1 | 1.3.1 | 1.3.1 | recipes | 0.1.6 | 0.1.17 | 0.1.17 | rematch | 1.0.1 | 1.0.1 | 1.0.1 | rematch2 | 2.1.2 | 2.1.2 | 2.1.2 | remotes | 2.1.1 | 2.4.2 | 2.4.2 | repr |
| 1.1.3 | 1.1.3 | reprex | 0.3.0 | 2.0.1 | 2.0.1 | reshape2 | 1.4.3 | 1.4.4 | 1.4.4 | reticulate | 1.15 | 1.22 | 1.22 | rex | 1.1.2 |
|
| rgexf |
| 0.16.2 | 0.16.2 | rhdf5 | 2.28.1 |
|
| Rhdf5lib | 1.6.3 |
|
| Rhtslib | 1.18.1 |
|
| rio |
| 0.5.29 | 0.5.29 | rjson |
| 0.2.20 | 0.2.20 | rlang | 0.4.6 | 0.4.12 | 0.4.12 | rmarkdown | 1.14 | 2.11 | 2.11 | ROCR | 1.0-7 |
|
| ROTS | 1.12.0 |
|
| roxygen2 | 7.1.0 |
|
| rpart | 4.1-15 | 4.1-15 | 4.1-15 | RPostgreSQL | 0.6-2 |
|
| rprojroot | 1.3-2 | 2.0.2 | 2.0.2 | Rsamtools | 2.2.1 |
|
| RSpectra | 0.15-0 |
|
| RSQLite | 2.1.2 |
|
| rstan | 2.19.2 |
|
| rstatix |
| 0.7.0 | 0.7.0 | rstudioapi | 0.11 | 0.13 | 0.13 | rsvd | 1.0.2 |
|
| rtracklayer | 1.44.4 |
|
| Rtsne | 0.15 |
|
| rversions | 2.0.1 |
|
| rvest | 0.3.4 | 1.0.2 | 1.0.2 | S4Vectors | 0.26.1 |
|
| sass |
| 0.4.0 | 0.4.0 | scales | 1.0.0 | 1.1.1 | 1.1.1 | scatterplot3d | 0.3-41 |
|
| sctransform | 0.2.0 |
|
| SDMTools | 1.1-221.1 |
|
| selectr | 0.4-1 | 0.4-2 | 0.4-2 | servr |
| 0.24 | 0.24 | sessioninfo | 1.1.1 |
|
| Seurat | 3.1.0 |
|
| shape |
| 1.4.6 | 1.4.6 | shiny | 1.3.2 | 1.7.1 | 1.7.1 | sitmo | 2.0.1 |
|
| sm | 2.2-5.6 |
|
| snakecase | 0.11.0 |
|
| snow | 0.4-3 | 0.4-4 | 0.4-4 | sourcetools | 0.1.7 | 0.1.7 | 0.1.7 | sp |
| 1.4-6 | 1.4-6 | sparklyr |
| 1.7.3 | 1.7.3 | SparseM |
| 1.81 | 1.81 | spatial |
| 7.3-14 | 7.3-14 | splines | 4.0.3 | 4.0.5 | 4.1.1 | splitstackshape | 1.4.8 |
|
| sqldf | 0.4-11 |
|
| SQUAREM | 2017.10-1 | 2021.1 | 2021.1 | StanHeaders | 2.18.1-10 |
|
| statmod | 1.4.32 | 1.4.36 | 1.4.36 | stats | 4.0.3 | 4.0.5 | 4.1.1 | stats4 | 4.0.3 | 4.0.5 | 4.1.1 | stringi | 1.4.3 | 1.7.6 | 1.7.6 | stringr | 1.4.0 | 1.4.0 | 1.4.0 | SummarizedExperiment | 1.18.2 |
|
| survival | 3.2-7 | 3.2-13 | 3.2-13 | svglite |
| 2.0.0 | 2.0.0 | sys | 3.2 | 3.4 | 3.4 | systemfonts |
| 1.0.3 | 1.0.3 | tcltk | 4.0.3 | 4.0.5 | 4.1.1 | terra |
|
| 1.4-22 | testthat | 2.3.2 | 3.1.1 | 3.1.1 | tibble | 2.1.3 | 3.1.6 | 3.1.6 | tidyr | 0.8.3 | 1.1.4 | 1.1.4 | tidyselect | 0.2.5 | 1.1.1 | 1.1.1 | tidyverse | 1.2.1 | 1.3.1 | 1.3.1 | timeDate | 3043.102 | 3043.102 | 3043.102 | tinytex | 0.15 | 0.35 | 0.35 | tools | 4.0.3 | 4.0.5 | 4.1.1 | triebeard |
| 0.3.0 | 0.3.0 | tsne | 0.1-3 |
|
| TTR | 0.23-4 | 0.24.2 | 0.24.2 | tweenr |
| 1.0.2 | 1.0.2 | tximport | 1.12.3 |
|
| tximportData | 1.18.0 |
|
| tzdb |
| 0.2.0 | 0.2.0 | urltools |
| 1.7.3 | 1.7.3 | usethis | 1.6.1 |
|
| utf8 | 1.1.4 | 1.2.2 | 1.2.2 | utils | 4.0.3 | 4.0.5 | 4.1.1 | uuid |
| 1.0-3 | 1.0-3 | uwot | 0.1.3 |
|
| vctrs | 0.2.0 | 0.3.8 | 0.3.8 | vioplot | 0.3.2 |
|
| viridis | 0.5.1 | 0.6.2 | 0.6.2 | viridisLite | 0.3.0 | 0.4.0 | 0.4.0 | visNetwork |
| 2.1.0 | 2.1.0 | vroom |
| 1.5.7 | 1.5.7 | waldo |
| 0.3.1 | 0.3.1 | webshot |
| 0.5.2 | 0.5.2 | whisker | 0.3-2 |
|
| withr | 2.2.0 | 2.4.3 | 2.4.3 | xfun | 0.8 | 0.28 | 0.28 | XML | 3.98-1.20 | 3.99-0.8 | 3.99-0.8 | xml2 | 1.3.2 | 1.3.3 | 1.3.3 | xopen | 1.0.0 |
|
| xtable | 1.8-4 | 1.8-4 | 1.8-4 | xts | 0.11-2 | 0.12.1 | 0.12.1 | XVector | 0.24.0 |
|
| yaml | 2.2.0 | 2.2.1 | 2.2.1 | zeallot | 0.1.0 |
|
| zip | 2.0.3 | 2.2.0 | 2.2.0 | zlibbioc | 1.30.0 |
|
| zoo | 1.8-6 | 1.8-9 | 1.8-9 |
|
A comprehensive list of packages is available in the RStudio singularity images. Click here to view the list and instructions for using them outside RStudio.
How to install R packages?
A variety of R packages are installed however it is recommended that users install packages (newer and updated versions) in their own home directory.
Start an interactive R session and install package using the command
| Code Block |
|---|
|
install.packages('packagename') |
Alternatively, you can add install.packages('packagename') within your R script. There are other tools to install packages such as BiocManager, pacman, devtools and remotes.
By default, R will try to install packages locally to ${HOME/x86_64-pc-linux-gnu-library. If you wish to use a different directory, then you need to set R_LIBS variable to point to that directory.
If you get an error installing packages locally, then use the command
| Code Block |
|---|
|
install.packages('packagename',lib=Sys.getenv("R_LIBS")) |
...