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
.inplaceReplaceLetterAt Man page
==,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
BStringSetToXStringQuality Source code
BStringToXStringQuality Source code
ByPos_MIndex-class Man page
ByPos_MIndex.combine Source code
Clongint.nbits 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
DNAorRNAcodes 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
H_recycle Source code
IUPAC_CODE_MAP Man page
IUPACcodes Source code
IlluminaQuality Man page Source code
IlluminaQuality-class Man page
InDel Man page
InDel-class Man page
IntegerOrNumericListToXStringQuality Source code
MIndex Man page
MIndex-class Man page
MTB_PDict Man page Source code
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
MaskedXString.codons Source code
MultipleAlignment Man page
MultipleAlignment-class Man page
MultipleAlignment.show_frame Source code
MultipleAlignment.show_frame_header Source code
MultipleAlignment.show_frame_line Source code
N50 Man page Source code
PAM120 Man page
PAM250 Man page
PAM30 Man page
PAM40 Man page
PAM70 Man page
PDict Man page Source code
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
PDict.showFirstLine Source code
PDict3Parts Man page Source code
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
PreprocessedTB.showFirstLine Source code
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 Source code
TB_PDict-class Man page
Twobit Man page
Twobit-class Man page
V_recycle Source code
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.amino_acid_frequency Source code
XString.codons Source code
XString.equal Source code
XString.lcprefix Source code
XString.lcsubstr Source code
XString.lcsuffix Source code
XString.letter_frequency Source code
XString.matchPWM Source code
XString.matchPattern Source code
XString.needwunsQS Source code
XString.nucleotide_frequency Source code
XString.read Source code
XString.readCodes Source code
XString.two_way_code_frequency Source code
XString.write Source code
XStringCodec Man page
XStringCodec-class Man page
XStringCodec.DNAorRNA Source code
XStringPartialMatches-class Man page
XStringQuality Man page
XStringQuality-class Man page
XStringQualityToInteger Source code
XStringQualityToIntegerMatrix Source code
XStringQualityToNumeric Source code
XStringSet Man page
XStringSet-class Man page
XStringSet-comparison Man page
XStringSet-io Man page
XStringSet.amino_acid_frequency Source code
XStringSet.letter_frequency Source code
XStringSet.match Source code
XStringSet.nucleotide_frequency Source code
XStringSet.pairwiseAlignment Source code
XStringSet.show_frame Source code
XStringSet.show_frame_header Source code
XStringSet.show_frame_line Source code
XStringSet.stringDist 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
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.matchPWM Source code
XStringViews.matchPattern 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
[,QualityScaledXStringSet-method Man page
[,XStringPartialMatches-method Man page
[[,ByPos_MIndex-method Man page
[[,PDict-method Man page
[[,SparseList-method Man page
aa2byte Source code
align-utils Man page
aligned Man page
aligned,AlignedXStringSet0-method Man page
aligned,PairwiseAlignmentsSingleSubject-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
alphabetFrequencyToUniqueLetters Source code
anyNA,XStringSet-method Man page
append,QualityScaledXStringSet,QualityScaledXStringSet-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
bsMismatch Source code
buildLookupTable Source code
charToXString Source code
charToXStringSet Source code
character.matchPattern Source code
characterToXStringQuality Source code
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
checkFormat Source code
checkMaxMismatch Source code
checkUserArgsWhenTrustedBandIsFull Source code
check_fasta_index Source code
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,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
coerce_and_call_next_method Source code
coerce_to Source code
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
combine.vwhich.compons Source code
combine.which.compons Source code
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
computeTrimEnd Source code
computeTrimStart Source code
compute_sorted_fasta_blocks_from_ssorted_fasta_index Source code
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
copySubSharedRaw Source code
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
dinucleotideFrequencyTest.XStringSet Source code
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
fasta.index Man page Source code
fasta.seqlengths Man page Source code
fastq.geometry Man page Source code
finalize_filexp_list 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
find_palindromes Source code
fromXStringViewsToStringSet Source code
from_MIndex_to_CompressedIRangesList 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_DNAorRNA_palindrome_L2R_lkup Source code
get_seqtype_conversion_lookup Man page Source code
get_xscat_ans_cardinality Source code
get_xscat_ans_seqtype 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
letterAsByteVal Source code
letterFrequency Man page Source code
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
makePipes Source code
makePostalignedSeqs Source code
makeSubstitutionLookupTable Source code
makeXStringFromSpaces Source code
makeXStringSetFrom2XStrings 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_fuzzy_genetic_code Source code
make_sequence_fillers_from_widths Source code
make_translation_lkup Source code
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
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
matchLRPatterns Man page
matchLRPatterns,MaskedXString-method Man page
matchLRPatterns,XString-method Man page
matchLRPatterns,XStringViews-method Man page
matchPDict Man page Source code
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
matchPattern.gregexpr Source code
matchPattern.gregexpr2 Source code
matchPatternAt Source code
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 Source code
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 Source code
mkAllStringsL Source code
mkAllStringsR Source code
mkOldToNewLkup 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 Source code
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
new_MultipleAlignment Source code
new_XStringSetList_from_List Source code
new_XStringSetList_from_list 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
normargAsArray Source code
normargCollapse Source code Source code
normargFastMovingSide Source code
normargFixed Source code
normargFuzzyMatrix Source code
normargLetters Source code
normargMaxMismatch Source code
normargMinMismatch Source code
normargMinScore Source code
normargOR Source code
normargPattern Source code
normargPfm Source code
normargPriorParams Source code
normargPwm Source code
normargSimplifyAs Source code
normargStep Source code
normargSubject Source code Source code
normargUseNames Source code
normargWidth Source code
normargWithIndels 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_skip Source code
normarg_value1 Source code
normarg_value2 Source code
nplaceReplaceLetterAt Source code
nrow,MultipleAlignment-method Man page
nsertSpaces Source code
ntegerToXStringQuality Source code
nucleotideFrequencyAt Man page
nucleotideFrequencyAt,XStringSet-method Man page
nucleotideFrequencyAt,XStringViews-method Man page
nucleotideSubstitutionMatrix Man page Source code
numericToXStringQuality 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
onLoad Source code
onUnload Source code
oneSeqToXStringSet 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
palindrome_arm_length Source code
parallelSlotNames,AlignedXStringSet0-method Man page
parallelVectorNames,AlignedXStringSet0-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
pcompare_XStringSet Source code
phiX174Phage Man page
pid Man page
pid,PairwiseAlignments-method Man page
pmatchPattern Man page Source code
pmatchPattern,XString-method Man page
pmatchPattern,XStringViews-method Man page
pmatchPattern,character-method Man page
pmatchPattern.rec Source code
postaligned_gap_ranges Source code
postaligned_match_ranges Source code
pow.int Source code
pre2postaligned 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
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
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
readRNAMultipleAlignment Man page Source code
readRNAStringSet Man page 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
reduceProbePairMatches 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
reverseComplement Man page
reverseComplement,DNAString-method Man page
reverseComplement,DNAStringSet-method Man page
reverseComplement,MaskedDNAString-method Man page
reverseComplement,MaskedRNAString-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
s_within_limits1 Source code
s_within_limits2 Source code
safe.subset.XStringSet Source code
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
setMask Source code
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
solve_id_or_name2 Source code
srPhiX174 Man page
stackStrings Man page Source code
start,AlignedXStringSet0-method Man page
startIndex Man page
startIndex,ByPos_MIndex-method Man page
strChop Source code
stringDist Man page
stringDist,QualityScaledXStringSet-method Man page
stringDist,XStringSet-method Man page
stringDist,character-method Man page
strsplit.useAsDefault Source code
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
test Source code
test.pre2postaligned Source code
threebands,character-method Man page
to.ans.type Source code
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 Source code
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
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
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
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 Man page Source code
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
wrap_msg Source code
write.MultAlign Source code
write.phylip Man page Source code
writePairHeader Source code
writePairSequences Source code
writePairwiseAlignments Man page Source code
writeXStringSet Man page Source code
write_XStringSet_to_fasta Source code
write_XStringSet_to_fastq 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 Source code
yeastSEQCHR1 Man page
Biostrings documentation built on Nov. 17, 2017, 9:26 a.m.