00datacache.R utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R
GENETIC_CODE.R XStringCodec-class.R seqtype.R XString-class.R
XStringSet-class.R XStringSet-comparison.R XStringViews-class.R
MaskedXString-class.R XStringSetList-class.R xscat.R
XStringSet-io.R letter.R getSeq.R dinucleotideFrequencyTest.R
chartr.R reverseComplement.R translate.R toComplex.R
replaceAt.R replaceLetterAt.R injectHardMask.R padAndClip.R
misc.R SparseList-class.R MIndex-class.R lowlevel-matching.R
match-utils.R matchPattern.R maskMotif.R matchPattern.BOC.R
matchPattern.BOC2.R matchLRPatterns.R trimLRPatterns.R
matchProbePair.R matchPWM.R findPalindromes.R PDict-class.R
matchPDict.R XStringPartialMatches-class.R
XStringQuality-class.R QualityScaledXStringSet.R
letterFrequency.R InDel-class.R AlignedXStringSet-class.R
PairwiseAlignments-class.R
PairwiseAlignmentsSingleSubject-class.R PairwiseAlignments-io.R
align-utils.R pmatchPattern.R pairwiseAlignment.R stringDist.R
needwunsQS.R MultipleAlignment.R matchprobes.R debug.R test.R
zzz.R

Representation and manipulation of genomic intervals

The ability to efficiently store genomic annotations and
	alignments is playing a central role when it comes to analyze
	high-throughput sequencing data (a.k.a. NGS data). The package
	defines general purpose containers for storing genomic intervals
	as well as more specialized containers for storing alignments
	against a reference genome.

methods, utils, stats, BiocGenerics, IRanges

AnnotationDbi (>= 1.21.1), AnnotationHub, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Dmelanogaster.UCSC.dm3, Biostrings (>= 2.25.3),
Rsamtools (>= 1.13.53), rtracklayer, KEGG.db, KEGGgraph,
GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene, seqnames.db, org.Sc.sgd.db,
VariantAnnotation, edgeR, DESeq, DEXSeq, pasilla,
pasillaBamSubset, RUnit, digest, BiocStyle

utils.R phicoef.R cigar-utils.R transcript-utils.R
constraint.R makeSeqnameIds.R seqinfo.R strand-utils.R
Seqinfo-class.R GenomicRanges-class.R GRanges-class.R
GIntervalTree-class.R GenomicRanges-comparison.R
GenomicRangesList-class.R GRangesList-class.R
makeGRangesFromDataFrame.R tileGenome.R GAlignments-class.R
GAlignmentPairs-class.R GAlignmentsList-class.R
SummarizedExperiment-class.R
SummarizedExperiment-rowData-methods.R seqlevels-utils.R
resolveHits-methods.R summarizeOverlaps.R
RangesMapping-methods.R RangedData-methods.R
intra-range-methods.R inter-range-methods.R setops-methods.R
findOverlaps-methods.R findOverlaps-GIntervalTree-methods.R
nearest-methods.R encodeOverlaps-methods.R coverage-methods.R
findSpliceOverlaps-methods.R findSpliceOverlaps-utils.R
test_GenomicRanges_package.R zzz.R