Files in Biostrings
Efficient manipulation of biological strings
TODO
CHANGES
README.md
NEWS
NAMESPACE
DESCRIPTION
build/vignette.rds
src/BitMatrix.c
src/XString_class.c
src/PreprocessedTB_class.c
src/align_utils.c
src/read_fastq_files.c
src/match_pdict.c
src/match_reporting.c
src/match_pdict_ACtree2.c
src/match_PWM.c
src/find_palindromes.c
src/unstrsplit_methods.c
src/replaceAt.c
src/match_pdict_Twobit.c
src/pmatchPattern.c
src/read_fasta_files.c
src/match_pattern_shiftor.c
src/lowlevel_matching.c
src/Biostrings.h
src/match_pattern_indels.c
src/matchprobes.c
src/RoSeqs_utils.c
src/utils.c
src/translate.c
src/SparseList_utils.c
src/S4Vectors_stubs.c
src/strutils.c
src/IRanges_stubs.c
src/match_pattern_boyermoore.c
src/XVector_stubs.c
src/XStringSet_class.c
src/inject_code.c
src/BAB_class.c
src/MIndex_class.c
src/R_init_Biostrings.c
src/align_needwunsQS.c
src/match_pattern.c
src/xscat.c
src/XStringSetList_class.c
src/match_pdict_utils.c
src/align_pairwiseAlignment.c
src/replace_letter_at.c
src/gtestsim.c
src/letter_frequency.c
data/srPhiX174.rda
data/phiX174Phage.rda
data/PAM70.rda
data/PAM250.rda
data/PAM30.rda
data/BLOSUM100.rda
data/BLOSUM45.rda
data/BLOSUM80.rda
data/yeastSEQCHR1.rda
data/BLOSUM62.rda
data/HNF4alpha.rda
data/BLOSUM50.rda
data/PAM120.rda
data/PAM40.rda
R/letterFrequency.R
R/AlignedXStringSet-class.R
R/xscat.R
R/pmatchPattern.R
R/InDel-class.R
R/findPalindromes.R
R/lowlevel-matching.R
R/XStringQuality-class.R
R/match-utils.R
R/misc.R
R/IUPAC_CODE_MAP.R
R/QualityScaledXStringSet.R
R/MaskedXString-class.R
R/XStringPartialMatches-class.R
R/utils.R
R/PDict-class.R
R/matchPattern.R
R/matchPWM.R
R/XStringViews-class.R
R/strsplit-methods.R
R/chartr.R
R/maskMotif.R
R/PairwiseAlignments-class.R
R/coloring.R
R/stringDist.R
R/dinucleotideFrequencyTest.R
R/PairwiseAlignments-io.R
R/getSeq.R
R/GENETIC_CODE.R
R/matchLRPatterns.R
R/XStringCodec-class.R
R/padAndClip.R
R/toComplex.R
R/zzz.R
R/matchprobes.R
R/PairwiseAlignmentsSingleSubject-class.R
R/pairwiseAlignment.R
R/matchProbePair.R
R/00datacache.R
R/needwunsQS.R
R/replaceLetterAt.R
R/seqtype.R
R/trimLRPatterns.R
R/align-utils.R
R/XStringSet-comparison.R
R/replaceAt.R
R/XString-class.R
R/reverseComplement.R
R/MultipleAlignment.R
R/matchPDict.R
R/letter.R
R/SparseList-class.R
R/XStringSet-io.R
R/XStringSetList-class.R
R/MIndex-class.R
R/XStringSet-class.R
R/injectHardMask.R
R/translate.R
R/AMINO_ACID_CODE.R
devtools/rgrep-tip.txt
vignettes/SolexaYi2-benchmark.txt
vignettes/BiostringsQuickOverview.Rnw
vignettes/PairwiseAlignments.Rnw
vignettes/Biostrings2Classes.Rnw
vignettes/MultipleAlignments.Rnw
vignettes/matchprobes.Rnw
man/HNF4alpha.Rd
man/replaceAt.Rd
man/gregexpr2.Rd
man/AAString-class.Rd
man/matchPDict-exact.Rd
man/IUPAC_CODE_MAP.Rd
man/phiX174Phage.Rd
man/dinucleotideFrequencyTest.Rd
man/letterFrequency.Rd
man/XStringPartialMatches-class.Rd
man/getSeq.Rd
man/translate.Rd
man/GENETIC_CODE.Rd
man/AMINO_ACID_CODE.Rd
man/MaskedXString-class.Rd
man/InDel-class.Rd
man/match-utils.Rd
man/xscat.Rd
man/XStringViews-class.Rd
man/findPalindromes.Rd
man/XString-class.Rd
man/Biostrings-internals.Rd
man/PairwiseAlignments-class.Rd
man/matchLRPatterns.Rd
man/stringDist.Rd
man/detail.Rd
man/pid.Rd
man/AlignedXStringSet-class.Rd
man/reverseComplement.Rd
man/MIndex-class.Rd
man/replaceLetterAt.Rd
man/injectHardMask.Rd
man/matchprobes.Rd
man/XStringSet-io.Rd
man/MultipleAlignment-class.Rd
man/pmatchPattern.Rd
man/align-utils.Rd
man/nucleotideFrequency.Rd
man/maskMotif.Rd
man/XStringSet-class.Rd
man/letter.Rd
man/padAndClip.Rd
man/toComplex.Rd
man/DNAString-class.Rd
man/substitution_matrices.Rd
man/yeastSEQCHR1.Rd
man/misc.Rd
man/matchPWM.Rd
man/QualityScaledXStringSet-class.Rd
man/longestConsecutive.Rd
man/lowlevel-matching.Rd
man/matchProbePair.Rd
man/PDict-class.Rd
man/pairwiseAlignment.Rd
man/trimLRPatterns.Rd
man/matchPDict-inexact.Rd
man/XStringQuality-class.Rd
man/PairwiseAlignments-io.Rd
man/needwunsQS.Rd
man/matchPattern.Rd
man/XStringSet-comparison.Rd
man/chartr.Rd
man/XStringSetList-class.Rd
man/RNAString-class.Rd
tests/run_unitTests.R
inst/doc/matchprobes.pdf
inst/doc/MultipleAlignments.pdf
inst/doc/BiostringsQuickOverview.Rnw
inst/doc/Biostrings2Classes.pdf
inst/doc/PairwiseAlignments.Rnw
inst/doc/PairwiseAlignments.pdf
inst/doc/Biostrings2Classes.Rnw
inst/doc/PairwiseAlignments.R
inst/doc/matchprobes.R
inst/doc/MultipleAlignments.Rnw
inst/doc/matchprobes.Rnw
inst/doc/MultipleAlignments.R
inst/doc/BiostringsQuickOverview.pdf
inst/doc/Biostrings2Classes.R
inst/extdata/Sc.fa
inst/extdata/someORF.fa.gz
inst/extdata/msx2_mRNA.aln
inst/extdata/dm3_upstream2000.fa.gz
inst/extdata/hg18chr8_gap.txt
inst/extdata/Sp.fa
inst/extdata/hg18chrY_gap.txt
inst/extdata/s_1_sequence.txt
inst/extdata/someORF.fa
inst/extdata/fastaEx.fa
inst/extdata/README
inst/extdata/Phylip.txt
inst/include/Biostrings_defines.h
inst/include/Biostrings_interface.h
inst/include/_Biostrings_stubs.c
inst/unitTests/test_findPalindromes.R
inst/unitTests/test_XStringSetList.R
inst/unitTests/test_matchDNAPattern.R.FIXME
inst/unitTests/test_pairwiseAlignment.R
inst/unitTests/test_XString.R
inst/unitTests/test_XStringSet.R
inst/unitTests/test_MultipleAlignment.R
inst/unitTests/test_matchPDict.R
inst/unitTests/test_twoWayAlphabetFrequency.R
