Biostrings
Efficient manipulation of biological strings

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1245
Source code
72
Man pages
64
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Biostrings: Efficient manipulation of biological strings
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API

API for Biostrings
Efficient manipulation of biological strings

Global functions
!=,BString,character-method Man page
!=,XString,XString-method Man page
!=,XString,XStringViews-method Man page
!=,XStringViews,XString-method Man page
!=,XStringViews,XStringViews-method Man page
!=,XStringViews,character-method Man page
!=,character,BString-method Man page
!=,character,XStringViews-method Man page
.BStringSetToXStringQuality Source code
.BStringToXStringQuality Source code
.Clongint.nbits Source code
.DNAorRNAcodes Source code
.H_recycle Source code
.IUPACcodes Source code
.IntegerOrNumericListToXStringQuality Source code
.MTB_PDict Source code
.MaskedXString.codons Source code
.PDict Source code
.PDict.showFirstLine Source code
.PDict3Parts Source code
.PreprocessedTB.showFirstLine Source code
.TB_PDict Source code
.V_recycle Source code
.XString.amino_acid_frequency Source code
.XString.codons Source code
.XString.equal Source code
.XString.letter_frequency Source code
.XString.matchPWM Source code
.XString.matchPattern Source code
.XString.nucleotide_frequency Source code
.XString.two_way_code_frequency Source code
.XStringCodec.DNAorRNA Source code
.XStringQualityToInteger Source code
.XStringQualityToIntegerMatrix Source code
.XStringQualityToNumeric Source code
.XStringSet.amino_acid_frequency Source code
.XStringSet.letter_frequency Source code
.XStringSet.match Source code
.XStringSet.nucleotide_frequency Source code
.XStringSet.show_frame Source code
.XStringSet.show_frame_header Source code
.XStringSet.show_frame_line Source code
.XStringSet.trimLRPatterns Source code
.XStringSet.two_way_code_frequency Source code
.XStringSet.two_way_code_frequency_by_quality Source code
.XStringSet.vmatchPattern Source code
.XStringSetAsViews Source code
.XStringViews.matchPWM Source code
.XStringViews.matchPattern Source code
.aa2byte Source code
.add_dna_and_rna_colors Source code
.alphabetFrequencyToUniqueLetters Source code
.bsMismatch Source code
.charToXString Source code
.charToXStringSet Source code
.character.matchPattern Source code
.characterToXStringQuality Source code
.checkFormat Source code
.checkMaxMismatch Source code
.checkUserArgsWhenTrustedBandIsFull Source code
.check_fasta_index Source code
.close_filexp_list Source code
.coerce_and_call_next_method Source code
.coerce_to Source code
.combine.vwhich.compons Source code
.combine.which.compons Source code
.computeTrimEnd Source code
.computeTrimStart Source code
.compute_sorted_fasta_blocks_from_ssorted_fasta_index Source code
.copySubSharedRaw Source code
.dinucleotideFrequencyTest.XStringSet Source code
.find_palindromes Source code
.from_MIndex_to_CompressedIRangesList Source code
.from_XStringQuality_to_CompressedIntegerList Source code
.from_XStringQuality_to_CompressedNumericList Source code
.get_DNAorRNA_palindrome_L2R_lkup Source code
.get_xscat_ans_cardinality Source code
.get_xscat_ans_seqtype Source code
.inplaceReplaceLetterAt Man page Source code
.insertSpaces Source code
.integerToXStringQuality Source code
.is_filexp_list Source code
.is_within_limits1 Source code
.is_within_limits2 Source code
.letterAsByteVal Source code
.letterFrequency Source code
.makePostalignedSeqs Source code
.makeSubstitutionLookupTable Source code
.make_CompressedIRangesList_from_IntegerList Source code
.make_CompressedIRangesList_from_at Source code
.make_IRanges_from_at Source code
.make_IRanges_from_numeric Source code
.make_XStringSetList_from_value Source code
.make_XStringSet_from_value Source code
.make_blank_BString Source code
.make_fuzzy_genetic_code Source code
.make_pipes Source code
.make_sequence_fillers_from_widths Source code
.make_translation_lkup Source code
.match.MTB_PDict Source code
.match.PDict3Parts.XString Source code
.match.PDict3Parts.XStringViews Source code
.match.TB_PDict Source code
.match.XStringSet Source code
.match.XStringSet.XString Source code
.match.XStringSet.XStringViews Source code
.matchPDict Source code
.matchPattern.gregexpr Source code
.matchPattern.gregexpr2 Source code
.matchPatternAt Source code
.mismatch Source code
.mkAllStrings Source code
.mkAllStringsL Source code
.mkAllStringsR Source code
.mkOldToNewLkup Source code
.needwunsQS Source code
.new_MultipleAlignment Source code
.new_XStringSetList_from_List Source code
.new_XStringSetList_from_list Source code
.normargAsArray Source code
.normargCollapse Source code
.normargFastMovingSide Source code
.normargFuzzyMatrix Source code
.normargLetters Source code
.normargMinScore Source code
.normargOR Source code
.normargPfm Source code
.normargPriorParams Source code
.normargPwm Source code
.normargSimplifyAs Source code
.normargStep Source code
.normargSubject Source code
.normargWidth Source code
.normargWithLabels Source code
.normarg_at1 Source code
.normarg_at2 Source code
.normarg_genetic.code Source code
.normarg_if.fuzzy.codon Source code
.normarg_maxLmismatch Source code
.normarg_nrec Source code
.normarg_padding.letter Source code
.normarg_quality Source code
.normarg_skip Source code
.normarg_value1 Source code
.normarg_value2 Source code
.numericToXStringQuality Source code
.onLoad Source code
.onUnload Source code
.oneSeqToXStringSet Source code
.palindrome_arm_length Source code
.pcompare_XStringSet Source code
.pmatchPattern Source code
.pmatchPattern.rec Source code
.postaligned_gap_ranges Source code
.postaligned_match_ranges Source code
.pre2postaligned Source code
.read.ClustalAln Source code
.read.MultipleAlignment Source code
.read.MultipleAlignment.splitRows Source code
.read.MultipleMask Source code
.read.PhylipAln Source code
.read.Stockholm Source code
.read_XStringSet Source code
.read_XStringSet_from_fasta_index Source code
.read_XStringSet_from_fastq Source code
.read_XStringSet_from_ssorted_fasta_index Source code
.read_fasta_files Source code
.read_fastq_files Source code
.setMask Source code
.show_PairwiseAlignments Source code
.solve_id_or_name2 Source code
.strChop Source code
.strsplit.useAsDefault Source code
.test Source code
.test.pre2postaligned Source code
.to.ans.type Source code
.translate Source code
.valid.AlignedXStringSet Source code
.valid.MaskedXString Source code
.valid.MaskedXString.masks Source code
.valid.MaskedXString.unmasked Source code
.valid.MultipleAlignment.colmask Source code
.valid.MultipleAlignment.rowmask Source code
.valid.MultipleAlignment.unmasked Source code
.valid.PairwiseAlignments Source code
.valid.QualityAlignedXStringSet Source code
.valid.QualityScaledXStringSet Source code
.valid.algos Source code
.vmatch.MTB_PDict Source code
.vmatch.PDict3Parts.XStringSet Source code
.vmatch.TB_PDict Source code
.vmatch.XStringSet Source code
.vmatch.XStringSet.XStringSet Source code
.vmatchPDict Source code
.wrap_msg Source code
.write.MultAlign Source code
.writePairHeader Source code
.writePairSequences Source code
.write_XStringSet_to_fasta Source code
.write_XStringSet_to_fastq Source code
==,BString,character-method Man page
==,XString,XString-method Man page
==,XString,XStringViews-method Man page
==,XStringViews,XString-method Man page
==,XStringViews,XStringViews-method Man page
==,XStringViews,character-method Man page
==,character,BString-method Man page
==,character,XStringViews-method Man page
AAMultipleAlignment Man page Source code
AAMultipleAlignment-class Man page
AAString Man page Source code
AAString-class Man page
AAStringSet Man page Source code
AAStringSet-class Man page
AAStringSetList Man page Source code
AAStringSetList-class Man page
AA_ALPHABET Man page
AA_PROTEINOGENIC Man page
AA_STANDARD Man page
ACtree2 Man page
ACtree2-class Man page
AMINO_ACID_CODE Man page
AlignedXStringSet Man page
AlignedXStringSet-class Man page
AlignedXStringSet0 Man page
AlignedXStringSet0-class Man page
BLOSUM100 Man page
BLOSUM45 Man page
BLOSUM50 Man page
BLOSUM62 Man page
BLOSUM80 Man page
BString Man page Source code
BString-class Man page
BStringSet Man page Source code
BStringSet-class Man page
BStringSetList Man page Source code
BStringSetList-class Man page
ByPos_MIndex-class Man page
ByPos_MIndex.combine Source code
DNAMultipleAlignment Man page Source code
DNAMultipleAlignment-class Man page
DNAString Man page Source code
DNAString-class Man page
DNAStringSet Man page Source code
DNAStringSet-class Man page
DNAStringSetList Man page Source code
DNAStringSetList-class Man page
DNA_ALPHABET Man page
DNA_BASES Man page
DNAcodes Source code
Expanded_TB_PDict Man page
Expanded_TB_PDict-class Man page
GENETIC_CODE Man page
GENETIC_CODE_TABLE Man page
HNF4alpha Man page
IUPAC_CODE_MAP Man page
IlluminaQuality Man page Source code
IlluminaQuality-class Man page
InDel Man page
InDel-class Man page
MIndex Man page
MIndex-class Man page
MTB_PDict Man page
MTB_PDict-class Man page
MaskedAAString Man page
MaskedAAString-class Man page
MaskedBString Man page
MaskedBString-class Man page
MaskedDNAString Man page
MaskedDNAString-class Man page
MaskedRNAString Man page
MaskedRNAString-class Man page
MaskedXString Man page
MaskedXString-class Man page
MultipleAlignment Man page
MultipleAlignment-class Man page
N50 Man page Source code
PAM120 Man page
PAM250 Man page
PAM30 Man page
PAM40 Man page
PAM70 Man page
PDict Man page
PDict,AsIs-method Man page
PDict,DNAStringSet-method Man page
PDict,XStringViews-method Man page
PDict,character-method Man page
PDict,probetable-method Man page
PDict-class Man page
PDict3Parts Man page
PDict3Parts-class Man page
PWM Man page
PWM,DNAStringSet-method Man page
PWM,character-method Man page
PWM,matrix-method Man page
PWMscoreStartingAt Man page Source code
PairwiseAlignments Man page
PairwiseAlignments,XString,XString-method Man page
PairwiseAlignments,XStringSet,missing-method Man page
PairwiseAlignments,character,character-method Man page
PairwiseAlignments,character,missing-method Man page
PairwiseAlignments-class Man page
PairwiseAlignments-io Man page
PairwiseAlignmentsSingleSubject Man page
PairwiseAlignmentsSingleSubject,XString,XString-method Man page
PairwiseAlignmentsSingleSubject,XStringSet,missing-method Man page
PairwiseAlignmentsSingleSubject,character,character-method Man page
PairwiseAlignmentsSingleSubject,character,missing-method Man page
PairwiseAlignmentsSingleSubject-class Man page
PairwiseAlignmentsSingleSubjectSummary Man page
PairwiseAlignmentsSingleSubjectSummary-class Man page
PhredQuality Man page Source code
PhredQuality-class Man page
PreprocessedTB Man page
PreprocessedTB-class Man page
QualityAlignedXStringSet Man page
QualityAlignedXStringSet-class Man page
QualityScaledAAStringSet Man page Source code
QualityScaledAAStringSet-class Man page
QualityScaledBStringSet Man page Source code
QualityScaledBStringSet-class Man page
QualityScaledDNAStringSet Man page Source code
QualityScaledDNAStringSet-class Man page
QualityScaledRNAStringSet Man page Source code
QualityScaledRNAStringSet-class Man page
QualityScaledXStringSet Man page Source code
QualityScaledXStringSet-class Man page
QualityScaledXStringSet.pairwiseAlignment Source code
QualityScaledXStringSet.stringDist Source code
RNAMultipleAlignment Man page Source code
RNAMultipleAlignment-class Man page
RNAString Man page Source code
RNAString-class Man page
RNAStringSet Man page Source code
RNAStringSet-class Man page
RNAStringSetList Man page Source code
RNAStringSetList-class Man page
RNA_ALPHABET Man page
RNA_BASES Man page
RNA_GENETIC_CODE Man page
RNAcodes Source code
SolexaQuality Man page Source code
SolexaQuality-class Man page
SparseList Man page
SparseList-class Man page
TB_PDict Man page
TB_PDict-class Man page
Twobit Man page
Twobit-class Man page
Views,MaskedXString-method Man page
Views,PairwiseAlignmentsSingleSubject-method Man page
Views,XString-method Man page
Views,character-method Man page
XString Man page
XString-class Man page
XString.lcprefix Source code
XString.lcsubstr Source code
XString.lcsuffix Source code
XString.needwunsQS Source code
XString.readCodes Source code
XStringCodec Man page
XStringCodec-class Man page
XStringPartialMatches-class Man page
XStringQuality Man page
XStringQuality-class Man page
XStringSet Man page
XStringSet-class Man page
XStringSet-comparison Man page
XStringSet-io Man page
XStringSet.pairwiseAlignment Source code
XStringSet.stringDist Source code
XStringSetList Man page Source code
XStringSetList-class Man page
XStringViews Man page
XStringViews-class Man page
XStringViews.equal Source code
XStringViews.get_snippet Source code
XStringViews.get_view Source code
XStringViews.show_vframe Source code
XStringViews.show_vframe_header Source code
XStringViews.show_vframe_line Source code
XStringViews.view1_equal_view2 Source code
[,XStringPartialMatches-method Man page
[[,ByPos_MIndex-method Man page
[[,PDict-method Man page
[[,SparseList-method Man page
add_colors Source code
align-utils Man page
aligned Man page
aligned,AlignedXStringSet0-method Man page
aligned,PairwiseAlignmentsSingleSubject-method Man page
alignedPattern Man page
alignedPattern,PairwiseAlignments-method Man page
alignedSubject Man page
alignedSubject,PairwiseAlignments-method Man page
alphabet Man page
alphabet,ANY-method Man page
alphabet,XStringQuality-method Man page
alphabetFrequency Man page
alphabetFrequency,AAString-method Man page
alphabetFrequency,AAStringSet-method Man page
alphabetFrequency,DNAString-method Man page
alphabetFrequency,DNAStringSet-method Man page
alphabetFrequency,MaskedXString-method Man page
alphabetFrequency,MultipleAlignment-method Man page
alphabetFrequency,RNAString-method Man page
alphabetFrequency,RNAStringSet-method Man page
alphabetFrequency,XString-method Man page
alphabetFrequency,XStringSet-method Man page
alphabetFrequency,XStringViews-method Man page
anyNA,XStringSet-method Man page
as.character,AlignedXStringSet0-method Man page
as.character,MaskedXString-method Man page
as.character,MultipleAlignment-method Man page
as.character,PairwiseAlignmentsSingleSubject-method Man page
as.character,XString-method Man page
as.character,XStringSet-method Man page
as.character,XStringViews-method Man page
as.data.frame,XStringSet-method Man page
as.data.frame,XStringViews-method Man page
as.factor,XStringSet-method Man page
as.list,MTB_PDict-method Man page
as.list,SparseList-method Man page
as.matrix,MultipleAlignment-method Man page
as.matrix,PairwiseAlignmentsSingleSubject-method Man page
as.matrix,XStringQuality-method Man page
as.matrix,XStringSet-method Man page
as.matrix,XStringViews-method Man page
as.vector,XString-method Man page
as.vector,XStringQuality-method Man page
as.vector,XStringSet-method Man page
buildLookupTable Source code
chartr Man page
chartr,ANY,ANY,MaskedXString-method Man page
chartr,ANY,ANY,XString-method Man page
chartr,ANY,ANY,XStringSet-method Man page
chartr,ANY,ANY,XStringViews-method Man page
class:AAMultipleAlignment Man page
class:AAString Man page
class:AAStringSet Man page
class:AAStringSetList Man page
class:ACtree2 Man page
class:AlignedXStringSet Man page
class:AlignedXStringSet0 Man page
class:BString Man page
class:BStringSet Man page
class:BStringSetList Man page
class:ByPos_MIndex Man page
class:DNAMultipleAlignment Man page
class:DNAString Man page
class:DNAStringSet Man page
class:DNAStringSetList Man page
class:Expanded_TB_PDict Man page
class:IlluminaQuality Man page
class:InDel Man page
class:MIndex Man page
class:MTB_PDict Man page
class:MaskedAAString Man page
class:MaskedBString Man page
class:MaskedDNAString Man page
class:MaskedRNAString Man page
class:MaskedXString Man page
class:MultipleAlignment Man page
class:PDict Man page
class:PDict3Parts Man page
class:PairwiseAlignments Man page
class:PairwiseAlignmentsSingleSubject Man page
class:PairwiseAlignmentsSingleSubjectSummary Man page
class:PhredQuality Man page
class:PreprocessedTB Man page
class:QualityAlignedXStringSet Man page
class:QualityScaledAAStringSet Man page
class:QualityScaledBStringSet Man page
class:QualityScaledDNAStringSet Man page
class:QualityScaledRNAStringSet Man page
class:QualityScaledXStringSet Man page
class:RNAMultipleAlignment Man page
class:RNAString Man page
class:RNAStringSet Man page
class:RNAStringSetList Man page
class:SolexaQuality Man page
class:SparseList Man page
class:TB_PDict Man page
class:Twobit Man page
class:XString Man page
class:XStringCodec Man page
class:XStringPartialMatches Man page
class:XStringQuality Man page
class:XStringSet Man page
class:XStringSetList Man page
class:XStringViews Man page
closestValues Source code
codons Man page
codons,DNAString-method Man page
codons,MaskedDNAString-method Man page
codons,MaskedRNAString-method Man page
codons,RNAString-method Man page
coerce,AAString,MaskedAAString-method Man page
coerce,ANY,AAStringSet-method Man page
coerce,ANY,BStringSet-method Man page
coerce,ANY,DNAStringSet-method Man page
coerce,ANY,RNAStringSet-method Man page
coerce,ANY,XStringSet-method Man page
coerce,BString,IlluminaQuality-method Man page
coerce,BString,MaskedBString-method Man page
coerce,BString,PhredQuality-method Man page
coerce,BString,SolexaQuality-method Man page
coerce,BStringSet,IlluminaQuality-method Man page
coerce,BStringSet,PhredQuality-method Man page
coerce,BStringSet,SolexaQuality-method Man page
coerce,DNAString,MaskedDNAString-method Man page
coerce,IntegerList,IlluminaQuality-method Man page
coerce,IntegerList,PhredQuality-method Man page
coerce,IntegerList,SolexaQuality-method Man page
coerce,MIndex,CompressedIRangesList-method Man page
coerce,MaskedAAString,AAString-method Man page
coerce,MaskedBString,BString-method Man page
coerce,MaskedDNAString,DNAString-method Man page
coerce,MaskedRNAString,RNAString-method Man page
coerce,MaskedXString,MaskCollection-method Man page
coerce,MaskedXString,MaskedAAString-method Man page
coerce,MaskedXString,MaskedBString-method Man page
coerce,MaskedXString,MaskedDNAString-method Man page
coerce,MaskedXString,MaskedRNAString-method Man page
coerce,MaskedXString,NormalIRanges-method Man page
coerce,MaskedXString,Views-method Man page
coerce,MaskedXString,XStringViews-method Man page
coerce,MultipleAlignment,AAStringSet-method Man page
coerce,MultipleAlignment,BStringSet-method Man page
coerce,MultipleAlignment,DNAStringSet-method Man page
coerce,MultipleAlignment,RNAStringSet-method Man page
coerce,NumericList,IlluminaQuality-method Man page
coerce,NumericList,PhredQuality-method Man page
coerce,NumericList,SolexaQuality-method Man page
coerce,RNAString,MaskedRNAString-method Man page
coerce,XString,AAString-method Man page
coerce,XString,BString-method Man page
coerce,XString,DNAString-method Man page
coerce,XString,RNAString-method Man page
coerce,XStringQuality,CompressedIntegerList-method Man page
coerce,XStringQuality,CompressedNumericList-method Man page
coerce,XStringQuality,IntegerList-method Man page
coerce,XStringQuality,NumericList-method Man page
coerce,XStringQuality,matrix-method Man page
coerce,XStringSet,Views-method Man page
coerce,XStringSet,XStringViews-method Man page
coerce,XStringViews,AAStringSet-method Man page
coerce,XStringViews,BStringSet-method Man page
coerce,XStringViews,DNAStringSet-method Man page
coerce,XStringViews,RNAStringSet-method Man page
coerce,XStringViews,XStringSet-method Man page
coerce,character,AAMultipleAlignment-method Man page
coerce,character,AAString-method Man page
coerce,character,BString-method Man page
coerce,character,DNAMultipleAlignment-method Man page
coerce,character,DNAString-method Man page
coerce,character,IlluminaQuality-method Man page
coerce,character,PhredQuality-method Man page
coerce,character,RNAMultipleAlignment-method Man page
coerce,character,RNAString-method Man page
coerce,character,SolexaQuality-method Man page
coerce,character,XString-method Man page
coerce,integer,IlluminaQuality-method Man page
coerce,integer,PhredQuality-method Man page
coerce,integer,SolexaQuality-method Man page
coerce,numeric,IlluminaQuality-method Man page
coerce,numeric,PhredQuality-method Man page
coerce,numeric,SolexaQuality-method Man page
collapse,MaskedXString-method Man page
colmask Man page
colmask,MultipleAlignment-method Man page
colmask<- Man page
colmask<-,MultipleAlignment,ANY-method Man page
colmask<-,MultipleAlignment,NULL-method Man page
comparable_seqtypes Source code
compareStrings Man page
compareStrings,AlignedXStringSet0,AlignedXStringSet0-method Man page
compareStrings,PairwiseAlignments,missing-method Man page
compareStrings,XString,XString-method Man page
compareStrings,XStringSet,XStringSet-method Man page
compareStrings,character,character-method Man page
compatible_seqtypes Source code
complement Man page
complement,DNAString-method Man page
complement,DNAStringSet-method Man page
complement,MaskedDNAString-method Man page
complement,MaskedRNAString-method Man page
complement,RNAString-method Man page
complement,RNAStringSet-method Man page
complement,XStringViews-method Man page
computeAllFlinks Man page
computeAllFlinks,ACtree2-method Man page
consensusMatrix Man page
consensusMatrix,MultipleAlignment-method Man page
consensusMatrix,PairwiseAlignmentsSingleSubject-method Man page
consensusMatrix,XStringSet-method Man page
consensusMatrix,XStringViews-method Man page
consensusMatrix,character-method Man page
consensusMatrix,matrix-method Man page
consensusString Man page
consensusString,AAMultipleAlignment-method Man page
consensusString,ANY-method Man page
consensusString,BStringSet-method Man page
consensusString,DNAMultipleAlignment-method Man page
consensusString,DNAStringSet-method Man page
consensusString,MultipleAlignment-method Man page
consensusString,RNAMultipleAlignment-method Man page
consensusString,RNAStringSet-method Man page
consensusString,XStringViews-method Man page
consensusString,matrix-method Man page
consensusViews Man page
consensusViews,AAMultipleAlignment-method Man page
consensusViews,DNAMultipleAlignment-method Man page
consensusViews,MultipleAlignment-method Man page
consensusViews,RNAMultipleAlignment-method Man page
countPDict Man page
countPDict,MaskedXString-method Man page
countPDict,XString-method Man page
countPDict,XStringSet-method Man page
countPDict,XStringViews-method Man page
countPWM Man page
countPWM,DNAString-method Man page
countPWM,MaskedDNAString-method Man page
countPWM,XStringViews-method Man page
countPWM,character-method Man page
countPattern Man page
countPattern,MaskedXString-method Man page
countPattern,XString-method Man page
countPattern,XStringSet-method Man page
countPattern,XStringViews-method Man page
countPattern,character-method Man page
coverage,AlignedXStringSet0-method Man page
coverage,MIndex-method Man page
coverage,MaskedXString-method Man page
coverage,PairwiseAlignmentsSingleSubject-method Man page
coverage,PairwiseAlignmentsSingleSubjectSummary-method Man page
createObject Source code
deletion Man page
deletion,InDel-method Man page
deletion,PairwiseAlignments-method Man page
detail Man page Source code
detail,MultipleAlignment-method Man page
dim,MultipleAlignment-method Man page
dinucleotideFrequency Man page Source code
dinucleotideFrequencyTest Man page
dinucleotideFrequencyTest,DNAStringSet-method Man page
dinucleotideFrequencyTest,RNAStringSet-method Man page
duplicated,PDict-method Man page
duplicated,PreprocessedTB-method Man page
elementNROWS,MIndex-method Man page
encoding Man page
encoding,XStringQuality-method Man page
end,AlignedXStringSet0-method Man page
endIndex Man page
endIndex,ByPos_MIndex-method Man page
errorSubstitutionMatrices Man page Source code
extractAllMatches Man page Source code
extractAt Man page
extractAt,XString-method Man page
extractAt,XStringSet-method Man page
extract_character_from_XString_by_positions Man page
extract_character_from_XString_by_positions,XString-method Man page
extract_character_from_XString_by_ranges Man page
extract_character_from_XString_by_ranges,XString-method Man page
fasta.index Man page Source code
fasta.seqlengths Man page Source code
fastq.geometry Man page Source code
fastq.seqlengths Man page Source code
findPalindromes Man page
findPalindromes,DNAString-method Man page
findPalindromes,MaskedXString-method Man page
findPalindromes,RNAString-method Man page
findPalindromes,XString-method Man page
findPalindromes,XStringViews-method Man page
fromXStringViewsToStringSet Source code
g.test Source code
gaps,MaskedXString-method Man page
getDNAComplementLookup Source code
getGeneticCode Man page Source code
getRNAComplementLookup Source code
getSeq Man page
get_aligned_pattern Source code
get_seqtype_conversion_lookup Man page Source code
getdata Source code
gregexpr2 Man page Source code
hasAllFlinks Man page
hasAllFlinks,ACtree2-method Man page
hasLetterAt Man page Source code
hasOnlyBaseLetters Man page
hasOnlyBaseLetters,DNAString-method Man page
hasOnlyBaseLetters,DNAStringSet-method Man page
hasOnlyBaseLetters,MaskedXString-method Man page
hasOnlyBaseLetters,RNAString-method Man page
hasOnlyBaseLetters,RNAStringSet-method Man page
hasOnlyBaseLetters,XStringViews-method Man page
head,PDict3Parts-method Man page
head,TB_PDict-method Man page
indel Man page
indel,AlignedXStringSet0-method Man page
indel,PairwiseAlignments-method Man page
initialize,ACtree2-method Man page
initialize,PreprocessedTB-method Man page
initialize,Twobit-method Man page
initialize,XStringCodec-method Man page
injectHardMask Man page
injectHardMask,MaskedXString-method Man page
injectHardMask,XStringViews-method Man page
insertion Man page
insertion,InDel-method Man page
insertion,PairwiseAlignments-method Man page
is.na,XStringSet-method Man page
isCharacterAlgo Source code
isMatchingAt Man page Source code
isMatchingEndingAt Man page
isMatchingEndingAt,XString-method Man page
isMatchingEndingAt,XStringSet-method Man page
isMatchingEndingAt,character-method Man page
isMatchingStartingAt Man page
isMatchingStartingAt,XString-method Man page
isMatchingStartingAt,XStringSet-method Man page
isMatchingStartingAt,character-method Man page
isNumericOrNAs Source code
lcprefix Man page
lcprefix,XString,XString-method Man page
lcprefix,XString,character-method Man page
lcprefix,character,XString-method Man page
lcprefix,character,character-method Man page
lcsubstr Man page
lcsubstr,XString,XString-method Man page
lcsubstr,XString,character-method Man page
lcsubstr,character,XString-method Man page
lcsubstr,character,character-method Man page
lcsuffix Man page
lcsuffix,XString,XString-method Man page
lcsuffix,XString,character-method Man page
lcsuffix,character,XString-method Man page
lcsuffix,character,character-method Man page
length,MIndex-method Man page
length,MaskedXString-method Man page
length,PDict-method Man page
length,PDict3Parts-method Man page
length,PairwiseAlignmentsSingleSubjectSummary-method Man page
length,PreprocessedTB-method Man page
length,SparseList-method Man page
letter Man page
letter,MaskedXString-method Man page
letter,XString-method Man page
letter,XStringViews-method Man page
letter,character-method Man page
letterFrequency Man page
letterFrequency,MaskedXString-method Man page
letterFrequency,XString-method Man page
letterFrequency,XStringSet-method Man page
letterFrequency,XStringViews-method Man page
letterFrequencyInSlidingView Man page
letterFrequencyInSlidingView,MaskedXString-method Man page
letterFrequencyInSlidingView,XString-method Man page
letterFrequencyInSlidingView,XStringSet-method Man page
letterFrequencyInSlidingView,XStringViews-method Man page
longestConsecutive Man page Source code
lowlevel-matching Man page
ls,SparseList-method Man page
make_DNA_AND_RNA_COLORED_LETTERS Source code
make_XStringSet_from_strings Man page
make_XStringSet_from_strings,XStringSet-method Man page
make_XString_from_string Man page
make_XString_from_string,XString-method Man page
mask Man page Source code
maskGaps Man page
maskGaps,MultipleAlignment-method Man page
maskMotif Man page
maskMotif,MaskedXString,XString-method Man page
maskMotif,MaskedXString,character-method Man page
maskMotif,MultipleAlignment,ANY-method Man page
maskMotif,XString,ANY-method Man page
maskeddim Man page
maskeddim,MultipleAlignment-method Man page
maskedncol Man page
maskedncol,MultipleAlignment-method Man page
maskednrow Man page
maskednrow,MultipleAlignment-method Man page
maskedratio,MaskedXString-method Man page
maskedratio,MultipleAlignment-method Man page
maskedwidth,MaskedXString-method Man page
masks Man page
masks,MaskedXString-method Man page
masks,XString-method Man page
masks<- Man page
masks<-,MaskedXString,MaskCollection-method Man page
masks<-,MaskedXString,NULL-method Man page
masks<-,XString,ANY-method Man page
masks<-,XString,NULL-method Man page
match,ANY,XStringSet-method Man page
match,XStringSet,ANY-method Man page
match,XStringSet,XStringSet-method Man page
match-utils Man page
matchLRPatterns Man page
matchLRPatterns,MaskedXString-method Man page
matchLRPatterns,XString-method Man page
matchLRPatterns,XStringViews-method Man page
matchPDict Man page
matchPDict,MaskedXString-method Man page
matchPDict,XString-method Man page
matchPDict,XStringSet-method Man page
matchPDict,XStringViews-method Man page
matchPDict-exact Man page
matchPDict-inexact Man page
matchPWM Man page
matchPWM,DNAString-method Man page
matchPWM,MaskedDNAString-method Man page
matchPWM,XStringViews-method Man page
matchPWM,character-method Man page
matchPattern Man page
matchPattern,MaskedXString-method Man page
matchPattern,XString-method Man page
matchPattern,XStringSet-method Man page
matchPattern,XStringViews-method Man page
matchPattern,character-method Man page
matchProbePair Man page
matchProbePair,DNAString-method Man page
matchProbePair,MaskedDNAString-method Man page
matchProbePair,XStringViews-method Man page
matchprobes Man page Source code
maxScore Man page
maxScore,ANY-method Man page
maxWeights Man page
maxWeights,matrix-method Man page
mergeIUPACLetters Man page Source code
minScore Man page
minScore,ANY-method Man page
minWeights Man page
minWeights,matrix-method Man page
misc Man page
mismatch Man page
mismatch,ANY,XStringViews-method Man page
mismatch,AlignedXStringSet0,missing-method Man page
mismatchSummary Man page
mismatchSummary,AlignedXStringSet0-method Man page
mismatchSummary,PairwiseAlignmentsSingleSubject-method Man page
mismatchSummary,PairwiseAlignmentsSingleSubjectSummary-method Man page
mismatchSummary,QualityAlignedXStringSet-method Man page
mismatchTable Man page
mismatchTable,AlignedXStringSet0-method Man page
mismatchTable,PairwiseAlignments-method Man page
mismatchTable,QualityAlignedXStringSet-method Man page
mkAllStrings Man page Source code
mpi.QualityScaledXStringSet.pairwiseAlignment Source code
mpi.XStringSet.pairwiseAlignment Source code
mpi.collate.pairwiseAlignment Source code
names,MIndex-method Man page
names,PDict-method Man page
names<-,MIndex-method Man page
names<-,PDict-method Man page
narrow,QualityScaledXStringSet-method Man page
narrow,character-method Man page
nchar,AlignedXStringSet0-method Man page
nchar,MaskedXString-method Man page
nchar,MultipleAlignment-method Man page
nchar,PairwiseAlignments-method Man page
nchar,PairwiseAlignmentsSingleSubjectSummary-method Man page
nchar,XString-method Man page
nchar,XStringSet-method Man page
nchar,XStringSetList-method Man page
nchar,XStringViews-method Man page
ncol,MultipleAlignment-method Man page
nedit Man page
nedit,PairwiseAlignments-method Man page
nedit,PairwiseAlignmentsSingleSubjectSummary-method Man page
neditAt Man page Source code
neditEndingAt Man page
neditEndingAt,XString-method Man page
neditEndingAt,XStringSet-method Man page
neditEndingAt,character-method Man page
neditStartingAt Man page
neditStartingAt,XString-method Man page
neditStartingAt,XStringSet-method Man page
neditStartingAt,character-method Man page
needwunsQS Man page
needwunsQS,XString,XString-method Man page
needwunsQS,XString,character-method Man page
needwunsQS,character,XString-method Man page
needwunsQS,character,character-method Man page
newPairwiseAlignments Source code
nindel Man page
nindel,AlignedXStringSet0-method Man page
nindel,PairwiseAlignments-method Man page
nindel,PairwiseAlignmentsSingleSubjectSummary-method Man page
nmatch Man page
nmatch,ANY,XStringViews-method Man page
nmatch,PairwiseAlignments,missing-method Man page
nmatch,PairwiseAlignmentsSingleSubjectSummary,missing-method Man page
nmismatch Man page
nmismatch,ANY,XStringViews-method Man page
nmismatch,AlignedXStringSet0,missing-method Man page
nmismatch,PairwiseAlignments,missing-method Man page
nmismatch,PairwiseAlignmentsSingleSubjectSummary,missing-method Man page
nnodes Man page
nnodes,ACtree2-method Man page
normargAlgorithm Source code
normargCollapse Source code
normargFixed Source code
normargMaxMismatch Source code
normargMinMismatch Source code
normargPattern Source code
normargSubject Source code
normargUseNames Source code
normargWithIndels Source code
nrow,MultipleAlignment-method Man page
nucleotideFrequencyAt Man page
nucleotideFrequencyAt,XStringSet-method Man page
nucleotideFrequencyAt,XStringViews-method Man page
nucleotideSubstitutionMatrix Man page Source code
oligonucleotideFrequency Man page Man page
oligonucleotideFrequency,MaskedXString-method Man page
oligonucleotideFrequency,XString-method Man page
oligonucleotideFrequency,XStringSet-method Man page
oligonucleotideFrequency,XStringViews-method Man page
oligonucleotideTransitions Man page Source code
padAndClip Man page Source code
pairwiseAlignment Man page
pairwiseAlignment,ANY,ANY-method Man page
pairwiseAlignment,ANY,QualityScaledXStringSet-method Man page
pairwiseAlignment,QualityScaledXStringSet,ANY-method Man page
pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSe Man page
palindromeArmLength Man page
palindromeArmLength,DNAString-method Man page
palindromeArmLength,RNAString-method Man page
palindromeArmLength,XString-method Man page
palindromeArmLength,XStringViews-method Man page
palindromeLeftArm Man page
palindromeLeftArm,XString-method Man page
palindromeLeftArm,XStringViews-method Man page
palindromeRightArm Man page
palindromeRightArm,XString-method Man page
palindromeRightArm,XStringViews-method Man page
parallelVectorNames,AlignedXStringSet0-method Man page
parallel_slot_names,AlignedXStringSet0-method Man page
parallel_slot_names,PairwiseAlignments-method Man page
parallel_slot_names,QualityScaledXStringSet-method Man page
pattern Man page
pattern,PairwiseAlignments-method Man page
pattern,XStringPartialMatches-method Man page
patternFrequency Man page
patternFrequency,PDict-method Man page
pcompare,ANY,XStringSet-method Man page
pcompare,XStringSet,ANY-method Man page
pcompare,XStringSet,XStringSet-method Man page
phiX174Phage Man page
pid Man page
pid,PairwiseAlignments-method Man page
pmatchPattern Man page
pmatchPattern,XString-method Man page
pmatchPattern,XStringViews-method Man page
pmatchPattern,character-method Man page
pow.int Source code
print.needwunsQS Man page Source code
quPhiX174 Man page
quality Man page
quality,QualityScaledXStringSet-method Man page
qualityConverter Source code
qualitySubstitutionMatrices Man page Source code
ranges,AlignedXStringSet0-method Man page
readAAMultipleAlignment Man page Source code
readAAStringSet Man page Source code
readBStringSet Man page Source code
readDNAMultipleAlignment Man page Source code
readDNAStringSet Man page Source code
readQualityScaledDNAStringSet Man page Source code
readRNAMultipleAlignment Man page Source code
readRNAStringSet Man page Source code
reduceProbePairMatches Source code
replaceAmbiguities Man page Source code
replaceAt Man page
replaceAt,XString-method Man page
replaceAt,XStringSet-method Man page
replaceLetterAt Man page
replaceLetterAt,DNAString-method Man page
replaceLetterAt,DNAStringSet-method Man page
reverse,MaskedXString-method Man page
reverse,QualityScaledXStringSet-method Man page
reverseComplement Man page
reverseComplement,DNAString-method Man page
reverseComplement,DNAStringSet-method Man page
reverseComplement,MaskedDNAString-method Man page
reverseComplement,MaskedRNAString-method Man page
reverseComplement,QualityScaledDNAStringSet-method Man page
reverseComplement,QualityScaledRNAStringSet-method Man page
reverseComplement,RNAString-method Man page
reverseComplement,RNAStringSet-method Man page
reverseComplement,XStringViews-method Man page
reverseComplement,matrix-method Man page
rowmask Man page
rowmask,MultipleAlignment-method Man page
rowmask<- Man page
rowmask<-,MultipleAlignment,ANY-method Man page
rowmask<-,MultipleAlignment,NULL-method Man page
rownames,MultipleAlignment-method Man page
rownames<-,MultipleAlignment-method Man page
safeLettersToInt Source code
saveXStringSet Man page Source code
score,PairwiseAlignments-method Man page
score,PairwiseAlignmentsSingleSubjectSummary-method Man page
selectAlgo Source code
seqtype Man page
seqtype,AAString-method Man page
seqtype,AlignedXStringSet0-method Man page
seqtype,BString-method Man page
seqtype,DNAString-method Man page
seqtype,MaskedXString-method Man page
seqtype,MultipleAlignment-method Man page
seqtype,PairwiseAlignments-method Man page
seqtype,RNAString-method Man page
seqtype,XStringSet-method Man page
seqtype,XStringSetList-method Man page
seqtype,XStringViews-method Man page
seqtype<- Man page
seqtype<-,MaskedXString-method Man page
seqtype<-,XString-method Man page
seqtype<-,XStringSet-method Man page
seqtype<-,XStringSetList-method Man page
seqtype<-,XStringViews-method Man page
show,ACtree2-method Man page
show,AlignedXStringSet0-method Man page
show,MIndex-method Man page
show,MTB_PDict-method Man page
show,MaskedXString-method Man page
show,MultipleAlignment-method Man page
show,PairwiseAlignments-method Man page
show,PairwiseAlignmentsSingleSubjectSummary-method Man page
show,QualityScaledXStringSet-method Man page
show,TB_PDict-method Man page
show,Twobit-method Man page
show,XString-method Man page
show,XStringPartialMatches-method Man page
show,XStringSet-method Man page
show,XStringSetList-method Man page
show,XStringViews-method Man page
showAsCell,XString-method Man page
showAsCell,XStringSet-method Man page
srPhiX174 Man page
stackStrings Man page Source code
start,AlignedXStringSet0-method Man page
startIndex Man page
startIndex,ByPos_MIndex-method Man page
stringDist Man page
stringDist,QualityScaledXStringSet-method Man page
stringDist,XStringSet-method Man page
stringDist,character-method Man page
subject,PairwiseAlignments-method Man page
subpatterns Man page
subpatterns,XStringPartialMatches-method Man page
subseq,MaskedXString-method Man page
subseq,character-method Man page
subseq<-,XStringSet-method Man page
subseq<-,character-method Man page
substitution.matrices Man page
substr,XString-method Man page
substring,XString-method Man page
summary,PairwiseAlignmentsSingleSubject-method Man page
tail,PDict3Parts-method Man page
tail,TB_PDict-method Man page
tb Man page
tb,PDict3Parts-method Man page
tb,PreprocessedTB-method Man page
tb,TB_PDict-method Man page
tb.width Man page
tb.width,PDict3Parts-method Man page
tb.width,PreprocessedTB-method Man page
tb.width,TB_PDict-method Man page
threebands,character-method Man page
toComplex Man page
toComplex,DNAString-method Man page
toSeqSnippet Source code
toString,AlignedXStringSet0-method Man page
toString,MaskedXString-method Man page
toString,PairwiseAlignmentsSingleSubject-method Man page
toString,XString-method Man page
toString,XStringSet-method Man page
toString,XStringViews-method Man page
toXStringViewsOrXString Source code
translate Man page
translate,DNAString-method Man page
translate,DNAStringSet-method Man page
translate,MaskedDNAString-method Man page
translate,MaskedRNAString-method Man page
translate,RNAString-method Man page
translate,RNAStringSet-method Man page
trimLRPatterns Man page
trimLRPatterns,XString-method Man page
trimLRPatterns,XStringSet-method Man page
trimLRPatterns,character-method Man page
trinucleotideFrequency Man page Source code
type Man page
type,PairwiseAlignments-method Man page
type,PairwiseAlignmentsSingleSubjectSummary-method Man page
unaligned Man page
unaligned,AlignedXStringSet0-method Man page
uniqueLetters Man page
uniqueLetters,MaskedXString-method Man page
uniqueLetters,XString-method Man page
uniqueLetters,XStringSet-method Man page
uniqueLetters,XStringViews-method Man page
unitScale Man page Source code
unlist,MIndex-method Man page
unlist,XStringSet-method Man page
unmasked Man page
unmasked,MaskedXString-method Man page
unmasked,MultipleAlignment-method Man page
unmasked,XString-method Man page
unsafe.newXStringViews Source code
updateObject,XString-method Man page
updateObject,XStringSet-method Man page
vcountPDict Man page
vcountPDict,MaskedXString-method Man page
vcountPDict,XString-method Man page
vcountPDict,XStringSet-method Man page
vcountPDict,XStringViews-method Man page
vcountPattern Man page
vcountPattern,MaskedXString-method Man page
vcountPattern,XString-method Man page
vcountPattern,XStringSet-method Man page
vcountPattern,XStringViews-method Man page
vcountPattern,character-method Man page
vmatchPDict Man page
vmatchPDict,ANY-method Man page
vmatchPDict,MaskedXString-method Man page
vmatchPDict,XString-method Man page
vmatchPattern Man page
vmatchPattern,MaskedXString-method Man page
vmatchPattern,XString-method Man page
vmatchPattern,XStringSet-method Man page
vmatchPattern,XStringViews-method Man page
vmatchPattern,character-method Man page
vwhichPDict Man page
vwhichPDict,MaskedXString-method Man page
vwhichPDict,XString-method Man page
vwhichPDict,XStringSet-method Man page
vwhichPDict,XStringViews-method Man page
which.isMatchingAt Man page Source code
which.isMatchingEndingAt Man page
which.isMatchingEndingAt,XString-method Man page
which.isMatchingEndingAt,XStringSet-method Man page
which.isMatchingEndingAt,character-method Man page
which.isMatchingStartingAt Man page
which.isMatchingStartingAt,XString-method Man page
which.isMatchingStartingAt,XStringSet-method Man page
which.isMatchingStartingAt,character-method Man page
whichPDict Man page
whichPDict,MaskedXString-method Man page
whichPDict,XString-method Man page
whichPDict,XStringSet-method Man page
whichPDict,XStringViews-method Man page
width,AlignedXStringSet0-method Man page
width,PDict-method Man page
width,PDict3Parts-method Man page
width,PreprocessedTB-method Man page
width,character-method Man page
width0 Man page
width0,MIndex-method Man page
windows,QualityScaledXStringSet-method Man page
windows,character-method Man page
write.phylip Man page Source code
writePairwiseAlignments Man page Source code
writeQualityScaledXStringSet Man page Source code
writeXStringSet Man page Source code
wtPhiX174 Man page
xs_dec_lkup Source code
xs_enc_lkup Source code
xsbaseclass Source code
xscat Man page Source code
xscodec Source code
xscodes Man page
xscodes,ANY-method Man page
yeastSEQCHR1 Man page
Biostrings documentation built on Nov. 8, 2020, 11:12 p.m.

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