r_packages
Installing Software
- Installation: Overview
- Downloads
- Installation: 'Site' installation
- Installation: MacOS GUI
- Installation: CLI Installer
- Available Packages
Using the BioGrids Environment
- Getting Started with BioGrids
- Overriding Software Versions
- BioGrids environment: Capsules
- BioGrids environment: Legacy
- BioGrids MacOS GUI : Usage
- BioGrids Package Manager : Usage
Getting Help
Support for Site Administrators
- Preparing Workstations to run the Software
- Managing your Installation
- Administrator Software Version Overrides
- Admins Mailing List
Hardware Support Notes
Available R Packages
Individual R packages are not listed in the BioGrids Supported Applications sotware list as they are too numerous.
R packages for the latest version of R are detailed in the table below.
A complete install of all Bioconductor packages is also available for site-wide installations.
| Package Version | R Version | |
|---|---|---|
| acepack | 1.4.1 | 3.5.1 |
| ade4 | 1.7-13 | 3.5.1 |
| alakazam | 0.2.11 | 3.5.1 |
| AneuFinderData | 1.10.0 | 3.5.1 |
| AnnotationDbi | 1.44.0 | 3.5.1 |
| AnnotationFilter | 1.6.0 | 3.5.1 |
| AnnotationHub | 2.14.5 | 3.5.1 |
| ape | 5.3 | 3.5.1 |
| askpass | 1.1 | 3.5.1 |
| assertive | 0.3-5 | 3.5.1 |
| assertive.base | 0.0-7 | 3.5.1 |
| assertive.code | 0.0-3 | 3.5.1 |
| assertive.data | 0.0-3 | 3.5.1 |
| assertive.data.uk | 0.0-2 | 3.5.1 |
| assertive.data.us | 0.0-2 | 3.5.1 |
| assertive.datetimes | 0.0-2 | 3.5.1 |
| assertive.files | 0.0-2 | 3.5.1 |
| assertive.matrices | 0.0-2 | 3.5.1 |
| assertive.models | 0.0-2 | 3.5.1 |
| assertive.numbers | 0.0-2 | 3.5.1 |
| assertive.properties | 0.0-4 | 3.5.1 |
| assertive.reflection | 0.0-4 | 3.5.1 |
| assertive.sets | 0.0-3 | 3.5.1 |
| assertive.strings | 0.0-3 | 3.5.1 |
| assertive.types | 0.0-3 | 3.5.1 |
| assertthat | 0.2.1 | 3.5.1 |
| backports | 1.1.4 | 3.5.1 |
| base64enc | 0.1-3 | 3.5.1 |
| basejump | 0.7.2 | 3.5.1 |
| bcbioBase | 0.4.1 | 3.5.1 |
| bcbioSingleCell | 0.2.1 | 3.5.1 |
| BH | 1.69.0-1 | 3.5.1 |
| bibtex | 0.4.2 | 3.5.1 |
| Biobase | 2.42.0 | 3.5.1 |
| BiocGenerics | 0.28.0 | 3.5.1 |
| BiocManager | 1.30.4 | 3.5.1 |
| BiocParallel | 1.16.6 | 3.5.1 |
| BiocVersion | 3.8.0 | 3.5.1 |
| biomaRt | 2.38.0 | 3.5.1 |
| Biostrings | 2.50.2 | 3.5.1 |
| bit | 1.1-14 | 3.5.1 |
| bit64 | 0.9-7 | 3.5.1 |
| bitops | 1.0-6 | 3.5.1 |
| blob | 1.1.1 | 3.5.1 |
| broom | 0.5.2 | 3.5.1 |
| callr | 3.2.0 | 3.5.1 |
| caTools | 1.17.1.2 | 3.5.1 |
| cellranger | 1.1.0 | 3.5.1 |
| checkmate | 1.9.1 | 3.5.1 |
| cli | 1.1.0 | 3.5.1 |
| clipr | 0.6.0 | 3.5.1 |
| colorspace | 1.4-1 | 3.5.1 |
| cowplot | 0.9.4 | 3.5.1 |
| crayon | 1.3.4 | 3.5.1 |
| crosstalk | 1.0.0 | 3.5.1 |
| curl | 3.3 | 3.5.1 |
| data.table | 1.12.2 | 3.5.1 |
| DBI | 1.0.0 | 3.5.1 |
| dbplyr | 1.3.0 | 3.5.1 |
| DelayedArray | 0.8.0 | 3.5.1 |
| dendsort | 0.3.3 | 3.5.1 |
| DEoptimR | 1.0-8 | 3.5.1 |
| digest | 0.6.18 | 3.5.1 |
| diptest | 0.75-7 | 3.5.1 |
| DNAcopy | 1.56.0 | 3.5.1 |
| doParallel | 1.0.14 | 3.5.1 |
| doSNOW | 1.0.16 | 3.5.1 |
| dplyr | 0.8.0.1 | 3.5.1 |
| dtw | 1.20-1 | 3.5.1 |
| ecp | 3.1.1 | 3.5.1 |
| ellipsis | 0.1.0 | 3.5.1 |
| ensembldb | 2.6.8 | 3.5.1 |
| evaluate | 0.13 | 3.5.1 |
| fansi | 0.4.0 | 3.5.1 |
| fitdistrplus | 1.0-14 | 3.5.1 |
| flexmix | 2.3-15 | 3.5.1 |
| forcats | 0.4.0 | 3.5.1 |
| foreach | 1.4.4 | 3.5.1 |
| formatR | 1.6 | 3.5.1 |
| Formula | 1.2-3 | 3.5.1 |
| fpc | 2.1-11.1 | 3.5.1 |
| fs | 1.2.7 | 3.5.1 |
| futile.logger | 1.4.3 | 3.5.1 |
| futile.options | 1.0.1 | 3.5.1 |
| future | 1.12.0 | 3.5.1 |
| future.apply | 1.2.0 | 3.5.1 |
| gbRd | 0.4-11 | 3.5.1 |
| gdata | 2.18.0 | 3.5.1 |
| generics | 0.0.2 | 3.5.1 |
| GenomeInfoDb | 1.18.2 | 3.5.1 |
| GenomeInfoDbData | 1.2.0 | 3.5.1 |
| GenomicAlignments | 1.18.1 | 3.5.1 |
| GenomicFeatures | 1.34.8 | 3.5.1 |
| GenomicRanges | 1.34.0 | 3.5.1 |
| GGally | 1.4.0 | 3.5.1 |
| ggdendro | 0.1-20 | 3.5.1 |
| ggplot2 | 3.1.1 | 3.5.1 |
| ggrepel | 0.8.0 | 3.5.1 |
| ggridges | 0.5.1 | 3.5.1 |
| globals | 0.12.4 | 3.5.1 |
| glue | 1.3.1 | 3.5.1 |
| gplots | 3.0.1.1 | 3.5.1 |
| gridExtra | 2.3 | 3.5.1 |
| grr | 0.9.5 | 3.5.1 |
| gtable | 0.3.0 | 3.5.1 |
| gtools | 3.8.1 | 3.5.1 |
| haven | 2.1.0 | 3.5.1 |
| hdf5r | 1.1.1 | 3.5.1 |
| hexbin | 1.27.2 | 3.5.1 |
| highr | 0.8 | 3.5.1 |
| Hmisc | 4.2-0 | 3.5.1 |
| hms | 0.4.2 | 3.5.1 |
| htmlTable | 1.13.1 | 3.5.1 |
| htmltools | 0.3.6 | 3.5.1 |
| htmlwidgets | 1.3 | 3.5.1 |
| httpuv | 1.5.1 | 3.5.1 |
| httr | 1.4.0 | 3.5.1 |
| ica | 1.0-2 | 3.5.1 |
| igraph | 1.2.4 | 3.5.1 |
| interactiveDisplayBase | 1.20.0 | 3.5.1 |
| IRanges | 2.16.0 | 3.5.1 |
| irlba | 2.3.3 | 3.5.1 |
| iterators | 1.0.10 | 3.5.1 |
| jsonlite | 1.6 | 3.5.1 |
| kedd | 1.0.3 | 3.5.1 |
| kernlab | 0.9-27 | 3.5.1 |
| knitr | 1.22 | 3.5.1 |
| labeling | 0.3 | 3.5.1 |
| lambda.r | 1.2.3 | 3.5.1 |
| lars | 1.2 | 3.5.1 |
| later | 0.8.0 | 3.5.1 |
| latticeExtra | 0.6-28 | 3.5.1 |
| lazyeval | 0.2.2 | 3.5.1 |
| listenv | 0.7.0 | 3.5.1 |
| lmtest | 0.9-36 | 3.5.1 |
| lsei | 1.2-0 | 3.5.1 |
| lubridate | 1.7.4 | 3.5.1 |
| magrittr | 1.5 | 3.5.1 |
| markdown | 0.9 | 3.5.1 |
| Matrix.utils | 0.9.7 | 3.5.1 |
| matrixStats | 0.54.0 | 3.5.1 |
| mclust | 5.4.3 | 3.5.1 |
| memoise | 1.1.0 | 3.5.1 |
| metap | 1.1 | 3.5.1 |
| mime | 0.6 | 3.5.1 |
| mixtools | 1.1.0 | 3.5.1 |
| modelr | 0.1.4 | 3.5.1 |
| modeltools | 0.2-22 | 3.5.1 |
| munsell | 0.5.0 | 3.5.1 |
| mvtnorm | 1.0-10 | 3.5.1 |
| npsurv | 0.4-0 | 3.5.1 |
| openssl | 1.3 | 3.5.1 |
| openxlsx | 4.1.0 | 3.5.1 |
| pbapply | 1.4-0 | 3.5.1 |
| pheatmap | 1.0.12 | 3.5.1 |
| pillar | 1.3.1 | 3.5.1 |
| pkgconfig | 2.0.2 | 3.5.1 |
| plogr | 0.2.0 | 3.5.1 |
| plotly | 4.9.0 | 3.5.1 |
| plyr | 1.8.4 | 3.5.1 |
| png | 0.1-7 | 3.5.1 |
| prabclus | 2.2-7 | 3.5.1 |
| prettyunits | 1.0.2 | 3.5.1 |
| processx | 3.3.0 | 3.5.1 |
| progress | 1.2.0 | 3.5.1 |
| promises | 1.0.1 | 3.5.1 |
| ProtGenerics | 1.14.0 | 3.5.1 |
| proxy | 0.4-23 | 3.5.1 |
| ps | 1.3.0 | 3.5.1 |
| purrr | 0.3.2 | 3.5.1 |
| R.methodsS3 | 1.7.1 | 3.5.1 |
| R.oo | 1.22.0 | 3.5.1 |
| R.utils | 2.8.0 | 3.5.1 |
| R6 | 2.4.0 | 3.5.1 |
| RANN | 2.6.1 | 3.5.1 |
| RColorBrewer | 1.1-2 | 3.5.1 |
| Rcpp | 1.0.1 | 3.5.1 |
| RcppEigen | 0.3.3.5.0 | 3.5.1 |
| RcppProgress | 0.4.1 | 3.5.1 |
| RCurl | 1.95-4.12 | 3.5.1 |
| Rdpack | 0.11-0 | 3.5.1 |
| rdrop2 | 0.8.1 | 3.5.1 |
| readr | 1.3.1 | 3.5.1 |
| readxl | 1.3.1 | 3.5.1 |
| rematch | 1.0.1 | 3.5.1 |
| remotes | 2.0.4 | 3.5.1 |
| ReorderCluster | 1.0 | 3.5.1 |
| reprex | 0.2.1 | 3.5.1 |
| reshape | 0.8.8 | 3.5.1 |
| reshape2 | 1.4.3 | 3.5.1 |
| reticulate | 1.12 | 3.5.1 |
| rhdf5 | 2.26.2 | 3.5.1 |
| rio | 0.5.16 | 3.5.1 |
| rlang | 0.3.4 | 3.5.1 |
| rmarkdown | 1.12 | 3.5.1 |
| robustbase | 0.93-4 | 3.5.1 |
| ROCR | 1.0-7 | 3.5.1 |
| Rsamtools | 1.34.1 | 3.5.1 |
| RSQLite | 2.1.1 | 3.5.1 |
| rstudioapi | 0.10 | 3.5.1 |
| rsvd | 1.0.0 | 3.5.1 |
| rtracklayer | 1.42.2 | 3.5.1 |
| Rtsne | 0.15 | 3.5.1 |
| rvest | 0.3.3 | 3.5.1 |
| S4Vectors | 0.20.1 | 3.5.1 |
| scales | 1.0.0 | 3.5.1 |
| scrm | 1.7.3-1 | 3.5.1 |
| sctransform | 0.2.0 | 3.5.1 |
| SDMTools | 1.1-221 | 3.5.1 |
| segmented | 0.5-3.0 | 3.5.1 |
| selectr | 0.4-1 | 3.5.1 |
| seqinr | 3.4-5 | 3.5.1 |
| sessioninfo | 1.1.1 | 3.5.1 |
| Seurat | 3.0.0 | 3.5.1 |
| shazam | 0.1.11 | 3.5.1 |
| shiny | 1.3.1 | 3.5.1 |
| SingleCellExperiment | 1.4.1 | 3.5.1 |
| snow | 0.4-3 | 3.5.1 |
| sourcetools | 0.1.7 | 3.5.1 |
| stringi | 1.4.3 | 3.5.1 |
| stringr | 1.4.0 | 3.5.1 |
| SummarizedExperiment | 1.12.0 | 3.5.1 |
| sys | 3.1 | 3.5.1 |
| tibble | 2.1.1 | 3.5.1 |
| tidyr | 0.8.3 | 3.5.1 |
| tidyselect | 0.2.5 | 3.5.1 |
| tidyverse | 1.2.1 | 3.5.1 |
| tigger | 0.3.1 | 3.5.1 |
| tinytex | 0.12 | 3.5.1 |
| trimcluster | 0.1-2.1 | 3.5.1 |
| tsne | 0.1-3 | 3.5.1 |
| utf8 | 1.1.4 | 3.5.1 |
| viridis | 0.5.1 | 3.5.1 |
| viridisLite | 0.3.0 | 3.5.1 |
| whisker | 0.3-2 | 3.5.1 |
| withr | 2.1.2 | 3.5.1 |
| xfun | 0.6 | 3.5.1 |
| XML | 3.98-1.19 | 3.5.1 |
| xml2 | 1.2.0 | 3.5.1 |
| xtable | 1.8-3 | 3.5.1 |
| XVector | 0.22.0 | 3.5.1 |
| yaml | 2.2.0 | 3.5.1 |
| zip | 2.0.1 | 3.5.1 |
| zlibbioc | 1.28.0 | 3.5.1 |
| zoo | 1.8-5 | 3.5.1 |
| base | 3.5.1 | 3.5.1 |
| boot | 1.3-20 | 3.5.1 |
| class | 7.3-15 | 3.5.1 |
| cluster | 2.0.8 | 3.5.1 |
| codetools | 0.2-16 | 3.5.1 |
| compiler | 3.5.1 | 3.5.1 |
| datasets | 3.5.1 | 3.5.1 |
| foreign | 0.8-71 | 3.5.1 |
| graphics | 3.5.1 | 3.5.1 |
| grDevices | 3.5.1 | 3.5.1 |
| grid | 3.5.1 | 3.5.1 |
| KernSmooth | 2.23-15 | 3.5.1 |
| lattice | 0.20-38 | 3.5.1 |
| MASS | 7.3-51.3 | 3.5.1 |
| Matrix | 1.2-17 | 3.5.1 |
| methods | 3.5.1 | 3.5.1 |
| mgcv | 1.8-28 | 3.5.1 |
| nlme | 3.1-139 | 3.5.1 |
| nnet | 7.3-12 | 3.5.1 |
| parallel | 3.5.1 | 3.5.1 |
| Rhdf5lib | 1.4.3 | 3.5.1 |
| rpart | 4.1-15 | 3.5.1 |
| spatial | 7.3-11 | 3.5.1 |
| splines | 3.5.1 | 3.5.1 |
| stats | 3.5.1 | 3.5.1 |
| stats4 | 3.5.1 | 3.5.1 |
| survival | 2.44-1.1 | 3.5.1 |
| tcltk | 3.5.1 | 3.5.1 |
| tools | 3.5.1 | 3.5.1 |
| utils | 3.5.1 | 3.5.1 |