r_packages.md
... ...
@@ -5,282 +5,143 @@ Individual R packages are not listed in the BioGrids Supported Applications sotw
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R packages for the latest version of R are detailed in the table below.
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A complete install of all Bioconductor packages is also available for site-wide installations.
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-| |Package Version |R Version |
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-|:----------------------|:---------------|:---------|
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-|acepack |1.4.1 |3.5.1 |
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-|ade4 |1.7-13 |3.5.1 |
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-|alakazam |0.2.11 |3.5.1 |
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-|AneuFinderData |1.10.0 |3.5.1 |
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-|AnnotationDbi |1.44.0 |3.5.1 |
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-|AnnotationFilter |1.6.0 |3.5.1 |
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-|AnnotationHub |2.14.5 |3.5.1 |
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-|ape |5.3 |3.5.1 |
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-|askpass |1.1 |3.5.1 |
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-|assertive |0.3-5 |3.5.1 |
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-|assertive.base |0.0-7 |3.5.1 |
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-|assertive.code |0.0-3 |3.5.1 |
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-|assertive.data |0.0-3 |3.5.1 |
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-|assertive.data.uk |0.0-2 |3.5.1 |
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-|assertive.data.us |0.0-2 |3.5.1 |
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-|assertive.datetimes |0.0-2 |3.5.1 |
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-|assertive.files |0.0-2 |3.5.1 |
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-|assertive.matrices |0.0-2 |3.5.1 |
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-|assertive.models |0.0-2 |3.5.1 |
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-|assertive.numbers |0.0-2 |3.5.1 |
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-|assertive.properties |0.0-4 |3.5.1 |
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-|assertive.reflection |0.0-4 |3.5.1 |
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-|assertive.sets |0.0-3 |3.5.1 |
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-|assertive.strings |0.0-3 |3.5.1 |
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-|assertive.types |0.0-3 |3.5.1 |
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-|assertthat |0.2.1 |3.5.1 |
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-|backports |1.1.4 |3.5.1 |
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-|base64enc |0.1-3 |3.5.1 |
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-|basejump |0.7.2 |3.5.1 |
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-|bcbioBase |0.4.1 |3.5.1 |
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-|bcbioSingleCell |0.2.1 |3.5.1 |
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-|BH |1.69.0-1 |3.5.1 |
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-|bibtex |0.4.2 |3.5.1 |
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-|Biobase |2.42.0 |3.5.1 |
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-|BiocGenerics |0.28.0 |3.5.1 |
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-|BiocManager |1.30.4 |3.5.1 |
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-|BiocParallel |1.16.6 |3.5.1 |
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-|BiocVersion |3.8.0 |3.5.1 |
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-|biomaRt |2.38.0 |3.5.1 |
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-|Biostrings |2.50.2 |3.5.1 |
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-|bit |1.1-14 |3.5.1 |
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-|bit64 |0.9-7 |3.5.1 |
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-|bitops |1.0-6 |3.5.1 |
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-|blob |1.1.1 |3.5.1 |
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-|broom |0.5.2 |3.5.1 |
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-|callr |3.2.0 |3.5.1 |
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-|caTools |1.17.1.2 |3.5.1 |
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-|cellranger |1.1.0 |3.5.1 |
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-|checkmate |1.9.1 |3.5.1 |
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-|cli |1.1.0 |3.5.1 |
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-|clipr |0.6.0 |3.5.1 |
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-|colorspace |1.4-1 |3.5.1 |
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-|cowplot |0.9.4 |3.5.1 |
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-|crayon |1.3.4 |3.5.1 |
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-|crosstalk |1.0.0 |3.5.1 |
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-|curl |3.3 |3.5.1 |
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-|data.table |1.12.2 |3.5.1 |
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-|DBI |1.0.0 |3.5.1 |
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-|dbplyr |1.3.0 |3.5.1 |
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-|DelayedArray |0.8.0 |3.5.1 |
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-|dendsort |0.3.3 |3.5.1 |
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-|DEoptimR |1.0-8 |3.5.1 |
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-|digest |0.6.18 |3.5.1 |
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-|diptest |0.75-7 |3.5.1 |
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-|DNAcopy |1.56.0 |3.5.1 |
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-|doParallel |1.0.14 |3.5.1 |
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-|doSNOW |1.0.16 |3.5.1 |
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-|dplyr |0.8.0.1 |3.5.1 |
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-|dtw |1.20-1 |3.5.1 |
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-|ecp |3.1.1 |3.5.1 |
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-|ellipsis |0.1.0 |3.5.1 |
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-|ensembldb |2.6.8 |3.5.1 |
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-|evaluate |0.13 |3.5.1 |
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-|fansi |0.4.0 |3.5.1 |
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-|fitdistrplus |1.0-14 |3.5.1 |
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-|flexmix |2.3-15 |3.5.1 |
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-|forcats |0.4.0 |3.5.1 |
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-|foreach |1.4.4 |3.5.1 |
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-|formatR |1.6 |3.5.1 |
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-|Formula |1.2-3 |3.5.1 |
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-|fpc |2.1-11.1 |3.5.1 |
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-|fs |1.2.7 |3.5.1 |
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-|futile.logger |1.4.3 |3.5.1 |
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-|futile.options |1.0.1 |3.5.1 |
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-|future |1.12.0 |3.5.1 |
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-|future.apply |1.2.0 |3.5.1 |
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-|gbRd |0.4-11 |3.5.1 |
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-|gdata |2.18.0 |3.5.1 |
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-|generics |0.0.2 |3.5.1 |
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-|GenomeInfoDb |1.18.2 |3.5.1 |
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-|GenomeInfoDbData |1.2.0 |3.5.1 |
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-|GenomicAlignments |1.18.1 |3.5.1 |
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-|GenomicFeatures |1.34.8 |3.5.1 |
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-|GenomicRanges |1.34.0 |3.5.1 |
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-|GGally |1.4.0 |3.5.1 |
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-|ggdendro |0.1-20 |3.5.1 |
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-|ggplot2 |3.1.1 |3.5.1 |
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-|ggrepel |0.8.0 |3.5.1 |
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-|ggridges |0.5.1 |3.5.1 |
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-|globals |0.12.4 |3.5.1 |
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-|glue |1.3.1 |3.5.1 |
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-|gplots |3.0.1.1 |3.5.1 |
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-|gridExtra |2.3 |3.5.1 |
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-|grr |0.9.5 |3.5.1 |
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-|gtable |0.3.0 |3.5.1 |
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-|gtools |3.8.1 |3.5.1 |
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-|haven |2.1.0 |3.5.1 |
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-|hdf5r |1.1.1 |3.5.1 |
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-|hexbin |1.27.2 |3.5.1 |
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-|highr |0.8 |3.5.1 |
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-|Hmisc |4.2-0 |3.5.1 |
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-|hms |0.4.2 |3.5.1 |
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-|htmlTable |1.13.1 |3.5.1 |
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-|htmltools |0.3.6 |3.5.1 |
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-|htmlwidgets |1.3 |3.5.1 |
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-|httpuv |1.5.1 |3.5.1 |
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-|httr |1.4.0 |3.5.1 |
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-|ica |1.0-2 |3.5.1 |
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-|igraph |1.2.4 |3.5.1 |
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-|interactiveDisplayBase |1.20.0 |3.5.1 |
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-|IRanges |2.16.0 |3.5.1 |
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-|irlba |2.3.3 |3.5.1 |
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-|iterators |1.0.10 |3.5.1 |
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-|jsonlite |1.6 |3.5.1 |
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-|kedd |1.0.3 |3.5.1 |
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-|kernlab |0.9-27 |3.5.1 |
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-|knitr |1.22 |3.5.1 |
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-|labeling |0.3 |3.5.1 |
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-|lambda.r |1.2.3 |3.5.1 |
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-|lars |1.2 |3.5.1 |
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-|later |0.8.0 |3.5.1 |
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-|latticeExtra |0.6-28 |3.5.1 |
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-|lazyeval |0.2.2 |3.5.1 |
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-|listenv |0.7.0 |3.5.1 |
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-|lmtest |0.9-36 |3.5.1 |
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-|lsei |1.2-0 |3.5.1 |
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-|lubridate |1.7.4 |3.5.1 |
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-|magrittr |1.5 |3.5.1 |
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-|markdown |0.9 |3.5.1 |
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-|Matrix.utils |0.9.7 |3.5.1 |
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-|matrixStats |0.54.0 |3.5.1 |
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-|mclust |5.4.3 |3.5.1 |
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-|memoise |1.1.0 |3.5.1 |
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-|metap |1.1 |3.5.1 |
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-|mime |0.6 |3.5.1 |
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-|mixtools |1.1.0 |3.5.1 |
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-|modelr |0.1.4 |3.5.1 |
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-|modeltools |0.2-22 |3.5.1 |
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-|munsell |0.5.0 |3.5.1 |
161
-|mvtnorm |1.0-10 |3.5.1 |
162
-|npsurv |0.4-0 |3.5.1 |
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-|openssl |1.3 |3.5.1 |
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-|openxlsx |4.1.0 |3.5.1 |
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-|pbapply |1.4-0 |3.5.1 |
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-|pheatmap |1.0.12 |3.5.1 |
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-|pillar |1.3.1 |3.5.1 |
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-|pkgconfig |2.0.2 |3.5.1 |
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-|plogr |0.2.0 |3.5.1 |
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-|plotly |4.9.0 |3.5.1 |
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-|plyr |1.8.4 |3.5.1 |
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-|png |0.1-7 |3.5.1 |
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-|prabclus |2.2-7 |3.5.1 |
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-|prettyunits |1.0.2 |3.5.1 |
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-|processx |3.3.0 |3.5.1 |
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-|progress |1.2.0 |3.5.1 |
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-|promises |1.0.1 |3.5.1 |
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-|ProtGenerics |1.14.0 |3.5.1 |
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-|proxy |0.4-23 |3.5.1 |
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-|ps |1.3.0 |3.5.1 |
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-|purrr |0.3.2 |3.5.1 |
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-|R.methodsS3 |1.7.1 |3.5.1 |
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-|R.oo |1.22.0 |3.5.1 |
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-|R.utils |2.8.0 |3.5.1 |
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-|R6 |2.4.0 |3.5.1 |
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-|RANN |2.6.1 |3.5.1 |
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-|RColorBrewer |1.1-2 |3.5.1 |
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-|Rcpp |1.0.1 |3.5.1 |
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-|RcppEigen |0.3.3.5.0 |3.5.1 |
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-|RcppProgress |0.4.1 |3.5.1 |
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-|RCurl |1.95-4.12 |3.5.1 |
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-|Rdpack |0.11-0 |3.5.1 |
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-|rdrop2 |0.8.1 |3.5.1 |
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-|readr |1.3.1 |3.5.1 |
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-|readxl |1.3.1 |3.5.1 |
196
-|rematch |1.0.1 |3.5.1 |
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-|remotes |2.0.4 |3.5.1 |
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-|ReorderCluster |1.0 |3.5.1 |
199
-|reprex |0.2.1 |3.5.1 |
200
-|reshape |0.8.8 |3.5.1 |
201
-|reshape2 |1.4.3 |3.5.1 |
202
-|reticulate |1.12 |3.5.1 |
203
-|rhdf5 |2.26.2 |3.5.1 |
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-|rio |0.5.16 |3.5.1 |
205
-|rlang |0.3.4 |3.5.1 |
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-|rmarkdown |1.12 |3.5.1 |
207
-|robustbase |0.93-4 |3.5.1 |
208
-|ROCR |1.0-7 |3.5.1 |
209
-|Rsamtools |1.34.1 |3.5.1 |
210
-|RSQLite |2.1.1 |3.5.1 |
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-|rstudioapi |0.10 |3.5.1 |
212
-|rsvd |1.0.0 |3.5.1 |
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-|rtracklayer |1.42.2 |3.5.1 |
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-|Rtsne |0.15 |3.5.1 |
215
-|rvest |0.3.3 |3.5.1 |
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-|S4Vectors |0.20.1 |3.5.1 |
217
-|scales |1.0.0 |3.5.1 |
218
-|scrm |1.7.3-1 |3.5.1 |
219
-|sctransform |0.2.0 |3.5.1 |
220
-|SDMTools |1.1-221 |3.5.1 |
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-|segmented |0.5-3.0 |3.5.1 |
222
-|selectr |0.4-1 |3.5.1 |
223
-|seqinr |3.4-5 |3.5.1 |
224
-|sessioninfo |1.1.1 |3.5.1 |
225
-|Seurat |3.0.0 |3.5.1 |
226
-|shazam |0.1.11 |3.5.1 |
227
-|shiny |1.3.1 |3.5.1 |
228
-|SingleCellExperiment |1.4.1 |3.5.1 |
229
-|snow |0.4-3 |3.5.1 |
230
-|sourcetools |0.1.7 |3.5.1 |
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-|stringi |1.4.3 |3.5.1 |
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-|stringr |1.4.0 |3.5.1 |
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-|SummarizedExperiment |1.12.0 |3.5.1 |
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-|sys |3.1 |3.5.1 |
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-|tibble |2.1.1 |3.5.1 |
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-|tidyr |0.8.3 |3.5.1 |
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-|tidyselect |0.2.5 |3.5.1 |
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-|tidyverse |1.2.1 |3.5.1 |
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-|tigger |0.3.1 |3.5.1 |
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-|tinytex |0.12 |3.5.1 |
241
-|trimcluster |0.1-2.1 |3.5.1 |
242
-|tsne |0.1-3 |3.5.1 |
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-|utf8 |1.1.4 |3.5.1 |
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-|viridis |0.5.1 |3.5.1 |
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-|viridisLite |0.3.0 |3.5.1 |
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-|whisker |0.3-2 |3.5.1 |
247
-|withr |2.1.2 |3.5.1 |
248
-|xfun |0.6 |3.5.1 |
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-|XML |3.98-1.19 |3.5.1 |
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-|xml2 |1.2.0 |3.5.1 |
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-|xtable |1.8-3 |3.5.1 |
252
-|XVector |0.22.0 |3.5.1 |
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-|yaml |2.2.0 |3.5.1 |
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-|zip |2.0.1 |3.5.1 |
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-|zlibbioc |1.28.0 |3.5.1 |
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-|zoo |1.8-5 |3.5.1 |
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-|base |3.5.1 |3.5.1 |
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-|boot |1.3-20 |3.5.1 |
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-|class |7.3-15 |3.5.1 |
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-|cluster |2.0.8 |3.5.1 |
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-|codetools |0.2-16 |3.5.1 |
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-|compiler |3.5.1 |3.5.1 |
263
-|datasets |3.5.1 |3.5.1 |
264
-|foreign |0.8-71 |3.5.1 |
265
-|graphics |3.5.1 |3.5.1 |
266
-|grDevices |3.5.1 |3.5.1 |
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-|grid |3.5.1 |3.5.1 |
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-|KernSmooth |2.23-15 |3.5.1 |
269
-|lattice |0.20-38 |3.5.1 |
270
-|MASS |7.3-51.3 |3.5.1 |
271
-|Matrix |1.2-17 |3.5.1 |
272
-|methods |3.5.1 |3.5.1 |
273
-|mgcv |1.8-28 |3.5.1 |
274
-|nlme |3.1-139 |3.5.1 |
275
-|nnet |7.3-12 |3.5.1 |
276
-|parallel |3.5.1 |3.5.1 |
277
-|Rhdf5lib |1.4.3 |3.5.1 |
278
-|rpart |4.1-15 |3.5.1 |
279
-|spatial |7.3-11 |3.5.1 |
280
-|splines |3.5.1 |3.5.1 |
281
-|stats |3.5.1 |3.5.1 |
282
-|stats4 |3.5.1 |3.5.1 |
283
-|survival |2.44-1.1 |3.5.1 |
284
-|tcltk |3.5.1 |3.5.1 |
285
-|tools |3.5.1 |3.5.1 |
286
-|utils |3.5.1 |3.5.1 |
8
+|Package|R 3.3.2 |R 3.5.1
9
+|---|---|---|
10
+|acepack|1.4.1|1.4.1|
11
+|ade4|1.7-10|1.7-13|
12
+|AnnotationDbi|1.36.2|1.44.0|
13
+|AnnotationHub|2.6.5|2.14.5|
14
+|askpass|1.1|1.1|
15
+|assertthat|0.2.1|0.2.1|
16
+|backports|1.1.2|1.1.4|
17
+|base|3.3.2|3.5.1|
18
+|base64enc|0.1-3|0.1-3|
19
+|BH|1.69.0-1|1.69.0-1|
20
+|Biobase|2.34.0|2.42.0|
21
+|BiocGenerics|0.20.0|0.28.0|
22
+|BiocParallel|1.8.2|1.16.6|
23
+|biomaRt|2.30.0|2.38.0|
24
+|Biostrings|2.42.1|2.50.2|
25
+|bit|1.1-12|1.1-14|
26
+|bit64|0.9-7|0.9-7|
27
+|bitops|1.0-6|1.0-6|
28
+|blob|1.1.0|1.1.1|
29
+|boot|1.3-20|1.3-20|
30
+|caTools|1.17.1|1.17.1.2|
31
+|checkmate|1.8.5|1.9.1|
32
+|class|7.3-14|7.3-15|
33
+|cli|1.0.0|1.1.0|
34
+|cluster|2.0.6|2.0.8|
35
+|codetools|0.2-15|0.2-16|
36
+|colorspace|1.3-2|1.4-1|
37
+|compiler|3.3.2|3.5.1|
38
+|crayon|1.3.4|1.3.4|
39
+|curl|3.3|3.3|
40
+|datasets|3.3.2|3.5.1|
41
+|data.table|1.10.4-3|1.12.2|
42
+|DBI|0.8|1.0.0|
43
+|digest|0.6.15|0.6.18|
44
+|dplyr|0.8.1|0.8.0.1|
45
+|ensembldb|1.6.2|2.6.8|
46
+|evaluate|0.10.1|0.13|
47
+|fansi|0.4.0|0.4.0|
48
+|foreign|0.8-69|0.8-71|
49
+|Formula|1.2-2|1.2-3|
50
+|futile.logger|1.4.3|1.4.3|
51
+|futile.options|1.0.0|1.0.1|
52
+|gdata|2.18.0|2.18.0|
53
+|GenomeInfoDb|1.10.3|1.18.2|
54
+|GenomicAlignments|1.10.1|1.18.1|
55
+|GenomicFeatures|1.26.4|1.34.8|
56
+|GenomicRanges|1.26.4|1.34.0|
57
+|ggplot2|2.2.1|3.1.1|
58
+|glue|1.3.1|1.3.1|
59
+|gplots|3.0.1|3.0.1.1|
60
+|graphics|3.3.2|3.5.1|
61
+|grDevices|3.3.2|3.5.1|
62
+|grid|3.3.2|3.5.1|
63
+|gridExtra|2.3|2.3|
64
+|gtable|0.2.0|0.3.0|
65
+|gtools|3.5.0|3.8.1|
66
+|highr|0.6|0.8|
67
+|Hmisc|4.1-1|4.2-0|
68
+|htmlTable|1.11.2|1.13.1|
69
+|htmltools|0.3.6|0.3.6|
70
+|htmlwidgets|1.0|1.3|
71
+|httpuv|1.5.1|1.5.1|
72
+|httr|1.4.0|1.4.0|
73
+|igraph|1.2.4.1|1.2.4|
74
+|interactiveDisplayBase|1.12.0|1.20.0|
75
+|IRanges|2.8.2|2.16.0|
76
+|jsonlite|1.5|1.6|
77
+|KernSmooth|2.23-15|2.23-15|
78
+|knitr|1.20|1.22|
79
+|labeling|0.3|0.3|
80
+|lambda.r|1.2|1.2.3|
81
+|later|0.8.0|0.8.0|
82
+|lattice|0.20-35|0.20-38|
83
+|latticeExtra|0.6-28|0.6-28|
84
+|lazyeval|0.2.1|0.2.2|
85
+|magrittr|1.5|1.5|
86
+|markdown|0.8|0.9|
87
+|MASS|7.3-49|7.3-51.3|
88
+|Matrix|1.2-12|1.2-17|
89
+|memoise|1.1.0|1.1.0|
90
+|methods|3.3.2|3.5.1|
91
+|mgcv|1.8-23|1.8-28|
92
+|mime|0.5|0.6|
93
+|munsell|0.4.3|0.5.0|
94
+|mvtnorm|1.0-7|1.0-10|
95
+|nlme|3.1-131.1|3.1-139|
96
+|nnet|7.3-12|7.3-12|
97
+|openssl|1.4|1.3|
98
+|Package|Version|Version|
99
+|parallel|3.3.2|3.5.1|
100
+|pheatmap|1.0.12|1.0.12|
101
+|pillar|1.4.1|1.3.1|
102
+|pkgconfig|2.0.2|2.0.2|
103
+|plogr|0.2.0|0.2.0|
104
+|plyr|1.8.4|1.8.4|
105
+|png|0.1-7|0.1-7|
106
+|promises|1.0.1|1.0.1|
107
+|purrr|0.3.2|0.3.2|
108
+|R6|2.4.0|2.4.0|
109
+|RColorBrewer|1.1-2|1.1-2|
110
+|Rcpp|1.0.1|1.0.1|
111
+|RCurl|1.95-4.10|1.95-4.12|
112
+|reshape2|1.4.3|1.4.3|
113
+|rlang|0.3.4|0.3.4|
114
+|rpart|4.1-13|4.1-15|
115
+|Rsamtools|1.26.2|1.34.1|
116
+|RSQLite|2.0|2.1.1|
117
+|rstudioapi|0.7|0.10|
118
+|rtracklayer|1.34.2|1.42.2|
119
+|S4Vectors|0.12.2|0.20.1|
120
+|scales|0.5.0|1.0.0|
121
+|shiny|1.3.2|1.3.1|
122
+|snow|0.4-2|0.4-3|
123
+|sourcetools|0.1.7|0.1.7|
124
+|spatial|7.3-11|7.3-11|
125
+|splines|3.3.2|3.5.1|
126
+|stats|3.3.2|3.5.1|
127
+|stats4|3.3.2|3.5.1|
128
+|stringi|1.1.7|1.4.3|
129
+|stringr|1.3.0|1.4.0|
130
+|SummarizedExperiment|1.4.0|1.12.0|
131
+|survival|2.41-3|2.44-1.1|
132
+|sys|3.2|3.1|
133
+|tcltk|3.3.2|3.5.1|
134
+|tibble|2.1.3|2.1.1|
135
+|tidyr|0.8.3|0.8.3|
136
+|tidyselect|0.2.5|0.2.5|
137
+|tools|3.3.2|3.5.1|
138
+|utf8|1.1.3|1.1.4|
139
+|utils|3.3.2|3.5.1|
140
+|viridis|0.5.0|0.5.1|
141
+|viridisLite|0.3.0|0.3.0|
142
+|withr|2.1.1|2.1.2|
143
+|xtable|1.8-2|1.8-3|
144
+|XVector|0.14.1|0.22.0|
145
+|yaml|2.1.18|2.2.0|
146
+|zlibbioc|1.20.0|1.28.0|
147
+|zoo|1.8-1|1.8-5|