Bioconductor/Biostrings
Efficient manipulation of biological strings

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Files in Bioconductor/Biostrings
Efficient manipulation of biological strings

.Rbuildignore
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/AMINO_ACID_CODE.R R/GENETIC_CODE.R R/IUPAC_CODE_MAP.R R/MIndex-class.R R/MaskedXString-class.R R/MultipleAlignment.R R/PDict-class.R R/QualityScaledXStringSet.R R/SparseList-class.R R/XString-class.R R/XStringCodec-class.R R/XStringPartialMatches-class.R R/XStringQuality-class.R R/XStringSet-class.R R/XStringSet-comparison.R R/XStringSet-io.R R/XStringSetList-class.R R/XStringViews-class.R R/chartr.R R/coloring.R R/dinucleotideFrequencyTest.R R/findPalindromes.R R/getSeq.R R/injectHardMask.R R/letter.R R/letterFrequency.R R/lowlevel-matching.R R/maskMotif.R R/match-utils.R R/matchLRPatterns.R R/matchPDict.R R/matchPWM.R R/matchPattern.R R/matchProbePair.R R/matchprobes.R R/misc.R R/moved_to_pwalign.R R/needwunsQS.R R/padAndClip.R R/pmatchPattern.R R/replaceAt.R R/replaceLetterAt.R R/reverseComplement.R R/seqinfo-methods.R R/seqtype.R R/strsplit-methods.R R/toComplex.R R/translate.R R/trimLRPatterns.R R/utils.R R/xscat.R R/zzz.R README.md
TODO
data/HNF4alpha.rda
data/yeastSEQCHR1.rda
inst/extdata/Phylip.txt
inst/extdata/README
inst/extdata/Sc.fa
inst/extdata/Sp.fa
inst/extdata/dm3_upstream2000.fa.gz
inst/extdata/fastaEx.fa
inst/extdata/hg18chr8_gap.txt
inst/extdata/hg18chrY_gap.txt
inst/extdata/msx2_mRNA.aln
inst/extdata/s_1_sequence.txt
inst/extdata/someORF.fa
inst/extdata/someORF.fa.gz
inst/include/Biostrings_defines.h
inst/include/Biostrings_interface.h
inst/include/_Biostrings_stubs.c
inst/unitTests/test_MultipleAlignment.R inst/unitTests/test_XString.R
inst/unitTests/test_matchDNAPattern.R.FIXME
inst/unitTests/test_seqinfo-methods.R inst/unitTests/test_twoWayAlphabetFrequency.R
legacy/CHANGES_Biostrings_2_vs_Biostrings_1
legacy/rgrep-tip.txt
man/AAString-class.Rd man/AMINO_ACID_CODE.Rd man/Biostrings-internals.Rd man/DNAString-class.Rd man/GENETIC_CODE.Rd man/HNF4alpha.Rd man/IUPAC_CODE_MAP.Rd man/MIndex-class.Rd man/MaskedXString-class.Rd man/MultipleAlignment-class.Rd man/PDict-class.Rd man/QualityScaledXStringSet-class.Rd man/RNAString-class.Rd man/XString-class.Rd man/XStringPartialMatches-class.Rd man/XStringQuality-class.Rd man/XStringSet-class.Rd man/XStringSet-comparison.Rd man/XStringSet-io.Rd man/XStringSetList-class.Rd man/XStringViews-class.Rd man/chartr.Rd man/detail.Rd man/dinucleotideFrequencyTest.Rd man/findPalindromes.Rd man/getSeq.Rd man/gregexpr2.Rd man/injectHardMask.Rd man/letter.Rd man/letterFrequency.Rd man/longestConsecutive.Rd man/lowlevel-matching.Rd man/maskMotif.Rd man/match-utils.Rd man/matchLRPatterns.Rd man/matchPDict-exact.Rd man/matchPDict-inexact.Rd man/matchPWM.Rd man/matchPattern.Rd man/matchProbePair.Rd man/matchprobes.Rd man/misc.Rd man/moved_to_pwalign.Rd man/needwunsQS.Rd man/nucleotideFrequency.Rd man/padAndClip.Rd man/pmatchPattern.Rd man/replaceAt.Rd man/replaceLetterAt.Rd man/reverseComplement.Rd man/seqinfo-methods.Rd man/toComplex.Rd man/translate.Rd man/trimLRPatterns.Rd man/xscat.Rd man/yeastSEQCHR1.Rd
src/BAB_class.c
src/Biostrings.h
src/BitMatrix.c
src/IRanges_stubs.c
src/MIndex_class.c
src/PreprocessedTB_class.c
src/R_init_Biostrings.c
src/RoSeqs_utils.c
src/S4Vectors_stubs.c
src/SparseList_utils.c
src/XStringSetList_class.c
src/XStringSet_class.c
src/XString_class.c
src/XVector_stubs.c
src/find_palindromes.c
src/gtestsim.c
src/inject_code.c
src/letter_frequency.c
src/lowlevel_matching.c
src/match_PWM.c
src/match_pattern.c
src/match_pattern_boyermoore.c
src/match_pattern_indels.c
src/match_pattern_shiftor.c
src/match_pdict.c
src/match_pdict_ACtree2.c
src/match_pdict_Twobit.c
src/match_pdict_utils.c
src/match_reporting.c
src/matchprobes.c
src/pmatchPattern.c
src/read_fasta_files.c
src/read_fastq_files.c
src/replaceAt.c
src/replace_letter_at.c
src/strutils.c
src/translate.c
src/unstrsplit_methods.c
src/utils.c
src/xscat.c
tests/testthat.R tests/testthat/test-MaskedXString.R tests/testthat/test-OtherMasking.R tests/testthat/test-PDict.R tests/testthat/test-QualityScaledXStringSet.R tests/testthat/test-XString-class.R tests/testthat/test-XStringQuality.R tests/testthat/test-XStringSet-class.R tests/testthat/test-XStringSet-io.R tests/testthat/test-XStringSetList-class.R tests/testthat/test-XStringSetList.R tests/testthat/test-XStringViews.R tests/testthat/test-chartr.R tests/testthat/test-dinucleotideFrequencyTest.R tests/testthat/test-findPalindromes.R tests/testthat/test-letter.R tests/testthat/test-letterFrequency.R tests/testthat/test-matchLRPatterns.R tests/testthat/test-matchPDict.R tests/testthat/test-matchPWM.R tests/testthat/test-matchPattern.R tests/testthat/test-miscXStringMethods.R tests/testthat/test-miscellaneous.R tests/testthat/test-replaceAt.R tests/testthat/test-translate.R tests/testthat/test-trimLRPatterns.R
vignettes/Biostrings2Classes.Rnw
vignettes/BiostringsQuickOverview.Rnw
vignettes/MultipleAlignments.Rmd
vignettes/PairwiseAlignments.Rnw
vignettes/SolexaYi2-benchmark.txt
vignettes/matchprobes.Rmd
Bioconductor/Biostrings documentation built on Nov. 11, 2024, 12:58 a.m.

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