Table 5. Selected packages based on the Ranges infrastructure.
Term | Count | Example packages |
Genetics | 16 | NarrowPeaks, nucleR, GenomicFeatures, mosaics |
Preprocessing | 11 | MEDIPS, biovizBase, TSSi, HMMcopy |
Infrastructure | 9 | Genominator, nnotationDbi, ggbio, dInfoBuilder |
GeneExpression | 8 | GGtools, easyRNASeq, Repitools, TransView |
Sequencing | 5 | girafe, triform, seqbias, rSFFreader |
Microarray | 4 | methyAnalysis, Gviz, MinimumDistance, charm |
Clustering | 4 | chroGPS, methVisual, DirichletMultinomial, PICS |
GenomicSequence | 3 | rGADEM, MotifDb, MotIV |
QualityControl | 3 | ShortRead, R453Plus1Toolbox, htSeqTools |
Statistics | 2 | oneChannelGUI, PING |
OneChannel | 2 | xmapcore, annmap |
DataRepresentation | 2 | genoset, FunciSNP |
GeneticVariability | 2 | VanillaICE, SNPchip |
Bioinformatics | 2 | DiffBind, segmentSeq |
ChIPseq | 2 | chipseq, BayesPeak |
Other | 10 | ChromHeatMap, gwascat, ChIPpeakAnno, OTUbase |
Categories are biocViews terms. Up to 4 packages were randomly sampled from Bioconductor packages that explicitly declare a dependence on IRanges, GenomicRanges, or GenomicFeatures packages.