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

Biostrings documentation built on Nov. 8, 2020, 11:12 p.m.