| affy | affyio | annotate | AnnotationDbi | backports |
| base | base64 | base64enc | beanplot | BH |
| Biobase | BiocGenerics | BiocInstaller | BiocParallel | biomaRt |
| Biostrings | bitops | blotter | boot | BSgenome |
| bumphunter | caTools | class | cluster | codetools |
| colorspace | compiler | crayon | curl | data.table |
| datasets | DBI | dichromat | digest | docopt |
| doRNG | edgeR | evaluate | ||
| fdrtool | fields | FinancialInstrument | foreach | foreign |
| formatR | futile.logger | futile.options | gdata | |
| genefilter | GenomeInfoDb | |||
| GenomicAlignments | GenomicFeatures | GenomicRanges | ||
| GEOquery | ggplot2 | gplots | graphics | grDevices |
| grid | gtable | gtools | HelloRanges | highr |
| htmltools | httr | illuminaio | IRanges | iterators |
| jsonlite | KernSmooth | knitr | labeling | lambda.r |
| lattice | lazyeval | limma | locfit | lumi |
| lumiHumanAll.db | magrittr | maps | markdown | |
| MASS | Matrix | matrixStats | ||
| mclust | memoise | methods | methylumi | mgcv |
| mime | minfi | multtest | munsell | nleqslv |
| nlme | nnet | nor1mix | openssl | org.Hs.eg.db |
| parallel | PerformanceAnalytics | pixmap | pkgmaker | plogr |
| plyr | praise | preprocessCore | quadprog | quantmod |
| quantstrat | R6 | raster | RColorBrewer | Rcpp |
| RCurl | registry | reshape | reshape2 | rgdal |
| rJava | rmarkdown | rngtools | rpart | rprojroot |
| Rsamtools | RSQLite | rtiff | rtracklayer | S4Vectors |
| scales | siggenes | snow | sp | spam |
| spatial | splines | stats | stats4 | stringi |
| stringr | SummarizedExperiment | survival | swirl | tcltk |
| testthat | tibble | tiff | tools | TTR |
| utils | VariantAnnotation | xlsx | xlsxjars | |
| XML | xtable | xts | XVector | yaml |
| zlibbioc | zoo |