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Title: String objects representing biological sequences, and matching
algorithms
Description: Memory efficient string containers, string matching
algorithms, and other utilities, for fast manipulation of large
biological sequences or sets of sequences.
Version: 2.42.1
Encoding: UTF-8
Author: H. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy
Maintainer: H. Pagès <hpages@fredhutch.org>
biocViews: SequenceMatching, Alignment, Sequencing, Genetics,
DataImport, DataRepresentation, Infrastructure
Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.6), S4Vectors (>=
0.11.1), IRanges (>= 2.5.27), XVector (>= 0.11.6)
Imports: graphics, methods, stats, utils, BiocGenerics, IRanges,
XVector
LinkingTo: S4Vectors, IRanges, XVector
Enhances: Rmpi
Suggests: 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
License: Artistic-2.0
LazyLoad: yes
Collate: 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
unstrsplit-methods.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 zzz.R
NeedsCompilation: yes
Packaged: 2016-11-30 23:13:14 UTC; biocbuild
Built: R 3.3.2; x86_64-pc-linux-gnu; 'Mon, 05 Dec 2016 13:05:07 +0100'; unix
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