_Sidebar.md
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@@ -5,9 +5,11 @@ Installing Software
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* [Supported Operating Systems](operatingsystems)
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* [Installation: 'Site' installation](installation_admin)
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* [Installation: MacOS GUI](client_install)
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-* [Installation: Package Manager](client_CLI_install)
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+* [Installation: CLI Installer](client_CLI_install)
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+* [Available Packages](https://biogrids.org/software/)
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+* [R Packages](r_packages)
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-Using the BIOGrids Environment
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+Using the BioGrids Environment
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* [Getting Started with BioGrids](getting_started)
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* [Overriding Software Versions](versions)
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* [BioGrids environment: Capsules](capsules)
r_packages.md
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+## Available R Packages
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+
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+Individual R packages are not listed in the [BioGrids Supported Applications](https://biogrids.org/software/) software list as they are too numerous.
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+
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+R packages for the current default version and the latest version of R are detailed in the table below.
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+
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+If you would like to use a package that is not currently available through BioGrids send a request to: help@biogrids.org.
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+
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+A complete install of all Bioconductor packages is also available for site-wide installations.
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+
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+
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+
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+|Package|R 3.3.2 |R 3.5.1
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+|---|---|---|
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+|acepack|1.4.1|1.4.1|
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+|ade4|1.7-10|1.7-13|
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+|AnnotationDbi|1.36.2|1.44.0|
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+|AnnotationHub|2.6.5|2.14.5|
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+|askpass|1.1|1.1|
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+|assertthat|0.2.1|0.2.1|
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+|backports|1.1.2|1.1.4|
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+|base|3.3.2|3.5.1|
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+|base64enc|0.1-3|0.1-3|
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+|BH|1.69.0-1|1.69.0-1|
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+|Biobase|2.34.0|2.42.0|
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+|BiocGenerics|0.20.0|0.28.0|
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+|BiocParallel|1.8.2|1.16.6|
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+|biomaRt|2.30.0|2.38.0|
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+|Biostrings|2.42.1|2.50.2|
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+|bit|1.1-12|1.1-14|
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+|bit64|0.9-7|0.9-7|
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+|bitops|1.0-6|1.0-6|
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+|blob|1.1.0|1.1.1|
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+|boot|1.3-20|1.3-20|
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+|caTools|1.17.1|1.17.1.2|
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+|checkmate|1.8.5|1.9.1|
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+|class|7.3-14|7.3-15|
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+|cli|1.0.0|1.1.0|
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+|cluster|2.0.6|2.0.8|
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+|codetools|0.2-15|0.2-16|
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+|colorspace|1.3-2|1.4-1|
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+|compiler|3.3.2|3.5.1|
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+|crayon|1.3.4|1.3.4|
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+|curl|3.3|3.3|
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+|datasets|3.3.2|3.5.1|
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+|data.table|1.10.4-3|1.12.2|
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+|DBI|0.8|1.0.0|
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+|digest|0.6.15|0.6.18|
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+|dplyr|0.8.1|0.8.0.1|
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+|ensembldb|1.6.2|2.6.8|
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+|evaluate|0.10.1|0.13|
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+|fansi|0.4.0|0.4.0|
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+|foreign|0.8-69|0.8-71|
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+|Formula|1.2-2|1.2-3|
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+|futile.logger|1.4.3|1.4.3|
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+|futile.options|1.0.0|1.0.1|
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+|gdata|2.18.0|2.18.0|
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+|GenomeInfoDb|1.10.3|1.18.2|
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+|GenomicAlignments|1.10.1|1.18.1|
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+|GenomicFeatures|1.26.4|1.34.8|
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+|GenomicRanges|1.26.4|1.34.0|
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+|ggplot2|2.2.1|3.1.1|
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+|glue|1.3.1|1.3.1|
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+|gplots|3.0.1|3.0.1.1|
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+|graphics|3.3.2|3.5.1|
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+|grDevices|3.3.2|3.5.1|
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+|grid|3.3.2|3.5.1|
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+|gridExtra|2.3|2.3|
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+|gtable|0.2.0|0.3.0|
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+|gtools|3.5.0|3.8.1|
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+|highr|0.6|0.8|
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+|Hmisc|4.1-1|4.2-0|
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+|htmlTable|1.11.2|1.13.1|
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+|htmltools|0.3.6|0.3.6|
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+|htmlwidgets|1.0|1.3|
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+|httpuv|1.5.1|1.5.1|
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+|httr|1.4.0|1.4.0|
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+|igraph|1.2.4.1|1.2.4|
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+|interactiveDisplayBase|1.12.0|1.20.0|
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+|IRanges|2.8.2|2.16.0|
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+|jsonlite|1.5|1.6|
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+|KernSmooth|2.23-15|2.23-15|
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+|knitr|1.20|1.22|
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+|labeling|0.3|0.3|
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+|lambda.r|1.2|1.2.3|
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+|later|0.8.0|0.8.0|
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+|lattice|0.20-35|0.20-38|
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+|latticeExtra|0.6-28|0.6-28|
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+|lazyeval|0.2.1|0.2.2|
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+|magrittr|1.5|1.5|
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+|markdown|0.8|0.9|
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+|MASS|7.3-49|7.3-51.3|
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+|Matrix|1.2-12|1.2-17|
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+|memoise|1.1.0|1.1.0|
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+|methods|3.3.2|3.5.1|
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+|mgcv|1.8-23|1.8-28|
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+|mime|0.5|0.6|
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+|munsell|0.4.3|0.5.0|
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+|mvtnorm|1.0-7|1.0-10|
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+|nlme|3.1-131.1|3.1-139|
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+|nnet|7.3-12|7.3-12|
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+|openssl|1.4|1.3|
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+|Package|Version|Version|
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+|parallel|3.3.2|3.5.1|
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+|pheatmap|1.0.12|1.0.12|
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+|pillar|1.4.1|1.3.1|
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+|pkgconfig|2.0.2|2.0.2|
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+|plogr|0.2.0|0.2.0|
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+|plyr|1.8.4|1.8.4|
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+|png|0.1-7|0.1-7|
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+|promises|1.0.1|1.0.1|
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+|purrr|0.3.2|0.3.2|
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+|R6|2.4.0|2.4.0|
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+|RColorBrewer|1.1-2|1.1-2|
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+|Rcpp|1.0.1|1.0.1|
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+|RCurl|1.95-4.10|1.95-4.12|
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+|reshape2|1.4.3|1.4.3|
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+|rlang|0.3.4|0.3.4|
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+|rpart|4.1-13|4.1-15|
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+|Rsamtools|1.26.2|1.34.1|
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+|RSQLite|2.0|2.1.1|
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+|rstudioapi|0.7|0.10|
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+|rtracklayer|1.34.2|1.42.2|
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+|S4Vectors|0.12.2|0.20.1|
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+|scales|0.5.0|1.0.0|
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+|shiny|1.3.2|1.3.1|
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+|snow|0.4-2|0.4-3|
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+|sourcetools|0.1.7|0.1.7|
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+|spatial|7.3-11|7.3-11|
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+|splines|3.3.2|3.5.1|
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+|stats|3.3.2|3.5.1|
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+|stats4|3.3.2|3.5.1|
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+|stringi|1.1.7|1.4.3|
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+|stringr|1.3.0|1.4.0|
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+|SummarizedExperiment|1.4.0|1.12.0|
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+|survival|2.41-3|2.44-1.1|
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+|sys|3.2|3.1|
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+|tcltk|3.3.2|3.5.1|
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+|tibble|2.1.3|2.1.1|
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+|tidyr|0.8.3|0.8.3|
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+|tidyselect|0.2.5|0.2.5|
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+|tools|3.3.2|3.5.1|
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+|utf8|1.1.3|1.1.4|
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+|utils|3.3.2|3.5.1|
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+|viridis|0.5.0|0.5.1|
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+|viridisLite|0.3.0|0.3.0|
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+|withr|2.1.1|2.1.2|
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+|xtable|1.8-2|1.8-3|
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+|XVector|0.14.1|0.22.0|
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+|yaml|2.1.18|2.2.0|
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+|zlibbioc|1.20.0|1.28.0|
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+|zoo|1.8-1|1.8-5|