Skip to main content
. 2013 Aug 8;9(8):e1003118. doi: 10.1371/journal.pcbi.1003118

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.