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

c(
	person("Hervé", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("Patrick", "Aboyoun", role="aut"),
	person("Robert", "Gentleman", role="aut"),
	person("Saikat", "DebRoy", role="aut"),
	person("Vince", "Carey", role="ctb"),
	person("Nicolas", "Delhomme", role="ctb"),
	person("Felix", "Ernst", role="ctb"),
	person("Haleema", "Khan", role="ctb",
	       comment="Converted 'matchprobes' vignette from Sweave to RMarkdown"),
	person("Aidan", "Lakshman", role="ctb"),
	person("Kieran", "O'Neill", role="ctb"),
	person("Valerie", "Obenchain", role="ctb"),
	person("Marcel", "Ramos", role="ctb"),
	person("Albert", "Vill", role="ctb"),
	person("Jen", "Wokaty", role="ctb",
	       comment="Converted 'matchprobes' vignette from Sweave to RMarkdown"),
	person("Erik", "Wright", role="ctb"))

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, BiocStyle, knitr

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