Efficient manipulation of biological strings
Memory efficient string containers, string matching
	algorithms, and other utilities, for fast manipulation of large
	biological sequences or sets of sequences.
SequenceMatching, Alignment, Sequencing, Genetics,
DataImport, DataRepresentation, Infrastructure
H. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy
methods, utils, grDevices, graphics, stats, crayon
BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=
1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,
hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy
(>= 1.41.3), affydata (>= 1.11.5), RUnit
00datacache.R utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R
GENETIC_CODE.R XStringCodec-class.R seqtype.R coloring.R
XString-class.R XStringSet-class.R XStringSet-comparison.R
XStringViews-class.R MaskedXString-class.R
XStringSetList-class.R seqinfo-methods.R xscat.R
XStringSet-io.R letter.R getSeq.R letterFrequency.R
dinucleotideFrequencyTest.R chartr.R reverseComplement.R
translate.R toComplex.R replaceAt.R replaceLetterAt.R
injectHardMask.R padAndClip.R strsplit-methods.R misc.R
SparseList-class.R MIndex-class.R lowlevel-matching.R
match-utils.R matchPattern.R maskMotif.R matchLRPatterns.R
trimLRPatterns.R matchProbePair.R matchPWM.R findPalindromes.R
PDict-class.R matchPDict.R XStringPartialMatches-class.R
XStringQuality-class.R QualityScaledXStringSet.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 zzz.R