Index

A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X

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A

AAString (class in bioc.biostrings) AAStringSet (class in bioc.biostrings) abstract (bioc.biobase.MIAME attribute) accession (bioc.geoquery.GEOData attribute) AlignedDataFrame (class in bioc.shortread) AlignedRead (class in bioc.shortread) AlignedXStringSet (class in bioc.biostrings) AlignedXStringSet0 (class in bioc.biostrings) alphabet (bioc.biostrings.AlignedXStringSet0 attribute) (bioc.biostrings.XString attribute) alphabetbycycle() (bioc.shortread.FastqQuality method) (bioc.shortread.ShortRead method) alphabetfrequency() (bioc.shortread.FastqQuality method) AnnDbBimap (class in bioc.annotationdbi) AnnDbMap (class in bioc.annotationdbi)

AnnotatedDataFrame (class in bioc.biobase) AnnotatedList (class in bioc.iranges) annotation() (bioc.biobase.ESet method) annotationdbi_conversion() (in module bioc.annotationdbi) append() (bioc.shortread.AlignedDataFrame method) ArrayIntensity (class in bioc.shortread) as_character() (bioc.biostrings.AlignedXStringSet0 method) as_DataFrame() (bioc.iranges.Ranges method) as_integer() (bioc.iranges.Ranges method) as_matrix() (bioc.biostrings.XStringViews method) (bioc.iranges.Ranges method) assaydata() (bioc.biobase.ESet method) AtomicList (class in bioc.iranges)

B

Bimap (class in bioc.annotationdbi) biobase_conversion() (in module bioc.biobase) bioc.annotationdbi (module) bioc.biobase (module) bioc.biostrings (module) bioc.bsgenome (module) bioc.geoquery (module) bioc.ggbase (module) bioc.ggtools (module)

bioc.gseabase (module) bioc.iranges (module) bioc.shortread (module) biostrings_conversion() (in module bioc.biostrings) BSgenome (class in bioc.bsgenome) bsgenome_conversion() (in module bioc.bsgenome) BString (class in bioc.biostrings) BStringSet (class in bioc.biostrings)

C

channel() (bioc.biobase.NChannelSet method) channelnames (bioc.biobase.NChannelSet attribute) CharacterList (class in bioc.iranges) CharacterOrMIAME (class in bioc.biobase) clean() (bioc.shortread.ShortRead method) collectiontype (bioc.gseabase.GeneSet attribute) coloring (bioc.gseabase.GeneColorSet attribute) columns (bioc.geoquery.GEOData attribute) (bioc.geoquery.GEODataTable attribute) combine() (bioc.biobase.AnnotatedDataFrame method)

ComplexList (class in bioc.iranges) CompressedAtomicList (class in bioc.iranges) contributor (bioc.gseabase.GeneSet attribute) count() (bioc.biostrings.PDict method) count_mappedkeys() (bioc.annotationdbi.Bimap method) coverage() (bioc.shortread.AlignedRead method) create_instance() (bioc.biostrings.PDict class method) creationdate (bioc.gseabase.GeneSet attribute)

D

DataFrame (class in bioc.iranges) datatable (bioc.geoquery.GEOData attribute) definition (bioc.annotationdbi.GOTerms attribute) deletion (bioc.biostrings.InDel attribute) description (bioc.gseabase.GeneSet attribute) detail() (bioc.shortread.ExperimentPath method) (bioc.shortread.QualityScore method) (bioc.shortread.RochePath method) (bioc.shortread.ShortRead method) (bioc.shortread.SolexaPath method)

difference() (bioc.gseabase.GeneSet method) DNAString (class in bioc.biostrings) DNAStringSet (class in bioc.biostrings)

E

end (bioc.biostrings.AlignedXStringSet0 attribute) (bioc.iranges.RangedData attribute) (bioc.iranges.Ranges attribute) esapply() (bioc.biobase.ExpressionSet method) ESet (class in bioc.biobase) experimentdata() (bioc.biobase.ESet method)

ExperimentPath (class in bioc.shortread) expinfo (bioc.biobase.MIAME attribute) ExpressionSet (class in bioc.biobase) exprs (bioc.biobase.ExpressionSet attribute) (bioc.ggbase.SmlSet attribute)

F

FastqQuality (class in bioc.shortread) featurenames (bioc.biobase.AnnotatedDataFrame attribute) fromCharacter_Character() (bioc.biostrings.PairwiseAlignedXStringSet static method)

fromCharacter_missing() (bioc.biostrings.PairwiseAlignedXStringSet static method) fromXString_XString() (bioc.biostrings.PairwiseAlignedXStringSet static method)

G

GDS (class in bioc.geoquery) genecolor (bioc.gseabase.GeneColorSet attribute) GeneColorSet (class in bioc.gseabase) geneids (bioc.gseabase.GeneSet attribute) (bioc.gseabase.GeneSetCollection attribute) geneidtype (bioc.gseabase.GeneSet attribute) GeneSet (class in bioc.gseabase) GeneSetCollection (class in bioc.gseabase) GeneSymbol (class in bioc.ggbase) GenomeData (class in bioc.bsgenome) GenomeDataList (class in bioc.bsgenome) GenomeDescription (class in bioc.bsgenome) GEOData (class in bioc.geoquery) GEODataTable (class in bioc.geoquery) geoquery_conversion() (in module bioc.geoquery) get_alphabet() (bioc.biostrings.AlignedXStringSet0 method) (bioc.biostrings.XString method) get_exprs() (bioc.biobase.ExpressionSet method) get_featuredata() (bioc.biobase.ESet method) get_featurenames() (bioc.biobase.AnnotatedDataFrame method) get_lkeys() (bioc.annotationdbi.AnnDbBimap method)

get_masks() (bioc.biostrings.MaskedXString method) get_names() (bioc.iranges.RangedData method) get_nchar() (bioc.biostrings.XStringViews method) get_pdata() (bioc.biobase.AnnotatedDataFrame method) get_phenodata() (bioc.biobase.ESet method) get_rkeys() (bioc.annotationdbi.AnnDbBimap method) get_subject() (bioc.iranges.Views method) get_tb() (bioc.biostrings.TB_PDict method) get_tb_width() (bioc.biostrings.TB_PDict method) get_unmasked() (bioc.biostrings.MaskedXString method) get_width() (bioc.iranges.MaskCollection method) getalleles() (bioc.ggbase.SmlSet method) ggbase_conversion() (in module bioc.ggbase) ggtools_conversion() (in module bioc.ggtools) GOID (bioc.annotationdbi.GOTerms attribute) GOTerms (class in bioc.annotationdbi) GPL (class in bioc.geoquery) gseabase_conversion() (in module bioc.gseabase) GSM (class in bioc.geoquery)

H

hybridizations (bioc.biobase.MIAME attribute)

I

InDel (class in bioc.biostrings) indel() (bioc.biostrings.AlignedXStringSet0 method) insertion (bioc.biostrings.InDel attribute) IntegerList (class in bioc.iranges) IntegerQuality (class in bioc.shortread) Intensity (class in bioc.shortread) IntensityInfo (class in bioc.shortread) IntensityMeasure (class in bioc.shortread) intersection() (bioc.gseabase.GeneSet method)

IntervalTree (class in bioc.iranges) IRanges (class in bioc.iranges) iranges_conversion() (in module bioc.iranges) IRangesList (class in bioc.iranges) isdisjoint() (bioc.iranges.Ranges method) isempty() (bioc.iranges.Ranges method) isnormal() (bioc.iranges.Ranges method)

K

keys() (bioc.annotationdbi.Bimap method)

L

lkeys (bioc.annotationdbi.AnnDbBimap attribute) LogicalList (class in bioc.iranges)

longdescription (bioc.gseabase.GeneSet attribute)

M

mappedkeys() (bioc.annotationdbi.Bimap method) mappedlkeys() (bioc.annotationdbi.AnnDbBimap method) mappedrkeys() (bioc.annotationdbi.AnnDbBimap method) MaskCollection (class in bioc.iranges) MaskedAAString (class in bioc.biostrings) MaskedBString (class in bioc.biostrings) MaskedDNAString (class in bioc.biostrings) MaskedRNAString (class in bioc.biostrings) MaskedXString (class in bioc.biostrings) masks (bioc.biostrings.MaskedXString attribute) match() (bioc.biostrings.PDict method)

MatrixQuality (class in bioc.shortread) max (bioc.iranges.NormalIRanges attribute) meta (bioc.geoquery.GEOData attribute) MIAME (class in bioc.biobase) mid() (bioc.iranges.Ranges method) min (bioc.iranges.NormalIRanges attribute) mseqnames (bioc.bsgenome.BSgenome attribute) MTB_PDict (class in bioc.biostrings) MultiSet (class in bioc.biobase)

N

name (bioc.gseabase.GeneSet attribute) names (bioc.gseabase.GeneSetCollection attribute) (bioc.iranges.RangedData attribute) narrow() (bioc.shortread.ShortRead method) NChannelSet (class in bioc.biobase) nchar (bioc.biostrings.AlignedXStringSet0 attribute) (bioc.biostrings.PairwiseAlignedXStringSet attribute) (bioc.biostrings.XString attribute) (bioc.biostrings.XStringViews attribute) new() (bioc.biobase.AnnotatedDataFrame class method) (bioc.biobase.ExpressionSet class method) (bioc.biostrings.AAString class method) (bioc.biostrings.AAStringSet class method) (bioc.biostrings.BString class method) (bioc.biostrings.BStringSet class method) (bioc.biostrings.DNAString class method) (bioc.biostrings.DNAStringSet class method) (bioc.biostrings.PhredQuality class method) (bioc.biostrings.QualityScaledAAStringSet class method) (bioc.biostrings.QualityScaledBStringSet class method) (bioc.biostrings.QualityScaledDNAStringSet class method) (bioc.biostrings.QualityScaledRNAStringSet class method) (bioc.biostrings.RNAString class method) (bioc.biostrings.RNAStringSet class method) (bioc.biostrings.SolexaQuality class method) (bioc.iranges.MaskCollection class method)

nindel (bioc.biostrings.PairwiseAlignedXStringSet attribute) NormalIRanges (class in bioc.iranges) normcontrols (bioc.biobase.MIAME attribute) notes (bioc.biobase.MIAME attribute) NumericList (class in bioc.iranges) NumericQuality (class in bioc.shortread)

O

ontology (bioc.annotationdbi.GOTerms attribute) organism (bioc.bsgenome.GenomeData attribute) (bioc.bsgenome.GenomeDescription attribute) (bioc.gseabase.GeneSet attribute)

otherinfo (bioc.biobase.MIAME attribute)

P

PairwiseAlignedFixedSubject (class in bioc.biostrings) PairwiseAlignedFixedSubjectSummary (class in bioc.biostrings) PairwiseAlignedXStringSet (class in bioc.biostrings) pattern (bioc.biostrings.PairwiseAlignedXStringSet attribute) pdata (bioc.biobase.AnnotatedDataFrame attribute) PDict (class in bioc.biostrings) phenotype() (bioc.gseabase.GeneColorSet method) phenotypecolor() (bioc.gseabase.GeneColorSet method)

PhredQuality (class in bioc.biostrings) preproc (bioc.biobase.MIAME attribute) provider (bioc.bsgenome.GenomeData attribute) (bioc.bsgenome.GenomeDescription attribute) provider_version (bioc.bsgenome.GenomeData attribute) (bioc.bsgenome.GenomeDescription attribute) pubmedids (bioc.gseabase.GeneSet attribute)

Q

QualityScaledAAStringSet (class in bioc.biostrings) QualityScaledBStringSet (class in bioc.biostrings) QualityScaledDNAStringSet (class in bioc.biostrings) QualityScaledRNAStringSet (class in bioc.biostrings)

QualityScaledXStringSet (class in bioc.biostrings) QualityScore (class in bioc.shortread)

R

RangedData (class in bioc.iranges) Ranges (class in bioc.iranges) RangesDataList (class in bioc.iranges) RangesList (class in bioc.iranges) RawList (class in bioc.iranges) read454() (bioc.shortread.RochePath method) readaligned() (bioc.shortread.SolexaPath method) readfasta() (bioc.shortread.RochePath method) readfastq() (bioc.shortread.SolexaPath method) readintensities() (bioc.shortread.SolexaPath method) readpath() (bioc.shortread.RochePath method) readprb() (bioc.shortread.SolexaPath method) readqseq() (bioc.shortread.SolexaPath method) readqual() (bioc.shortread.RochePath method) release_date (bioc.bsgenome.GenomeDescription attribute) release_name (bioc.bsgenome.GenomeDescription attribute) reverse() (bioc.biostrings.XString method)

reverse_complement() (bioc.biostrings.DNAString method) (bioc.biostrings.RNAString method) (bioc.biostrings.XStringViews method) rkeys (bioc.annotationdbi.AnnDbBimap attribute) Rle (class in bioc.iranges) RleViews (class in bioc.iranges) RNAString (class in bioc.biostrings) RNAStringSet (class in bioc.biostrings) RochePath (class in bioc.shortread) RocheSet (class in bioc.shortread) rocheset() (bioc.shortread.RochePath method) runnames() (bioc.shortread.RochePath method) rx() (bioc.gseabase.GeneColorSet method) (bioc.gseabase.GeneSet method) (bioc.shortread.AlignedRead method)

S

samples (bioc.biobase.MIAME attribute) score (bioc.biostrings.PairwiseAlignedXStringSet attribute) secondary (bioc.annotationdbi.GOTerms attribute) selectchannels() (bioc.biobase.NChannelSet method) seqlengths (bioc.bsgenome.BSgenome attribute) seqnames (bioc.bsgenome.BSgenome attribute) Sequence (class in bioc.iranges) set_exprs() (bioc.biobase.ExpressionSet method) set_featuredata() (bioc.biobase.ESet method) set_featurenames() (bioc.biobase.AnnotatedDataFrame method) set_lkeys() (bioc.annotationdbi.AnnDbBimap method) set_masks() (bioc.biostrings.MaskedXString method) set_pdata() (bioc.biobase.AnnotatedDataFrame method) set_phenodata() (bioc.biobase.ESet method) set_rkeys() (bioc.annotationdbi.AnnDbBimap method) SFastqQuality (class in bioc.shortread) ShortRead (class in bioc.shortread) shortread_conversion() (in module bioc.shortread) ShortReadQ (class in bioc.shortread) SimpleAtomicList (class in bioc.iranges) SimpleList (class in bioc.iranges) smlenv (bioc.ggbase.SmlSet attribute) smlist (bioc.ggbase.SmlSet attribute) SmlSet (class in bioc.ggbase) snps() (bioc.ggbase.SmlSet method)

SnpSet (class in bioc.biobase) SolexaIntensity (class in bioc.shortread) SolexaIntensityInfo (class in bioc.shortread) SolexaPath (class in bioc.shortread) SolexaQuality (class in bioc.biostrings) SolexaSet (class in bioc.shortread) solexaset() (bioc.shortread.SolexaPath method) species (bioc.bsgenome.GenomeDescription attribute) srduplicated() (bioc.shortread.FastqQuality method) (bioc.shortread.ShortRead method) srorder() (bioc.shortread.FastqQuality method) (bioc.shortread.ShortRead method) srrank() (bioc.shortread.FastqQuality method) (bioc.shortread.ShortRead method) SRSet (class in bioc.shortread) srsort() (bioc.shortread.ShortRead method) start (bioc.biostrings.AlignedXStringSet0 attribute) (bioc.iranges.RangedData attribute) (bioc.iranges.Ranges attribute) subject (bioc.iranges.Views attribute) subset() (bioc.annotationdbi.AnnDbBimap method) (bioc.annotationdbi.Bimap method) (bioc.biostrings.XStringSet method) synonym (bioc.annotationdbi.GOTerms attribute)

T

table (bioc.geoquery.GEOData attribute) (bioc.geoquery.GEODataTable attribute) tables() (bioc.shortread.ShortRead method) tb (bioc.biostrings.TB_PDict attribute)

TB_PDict (class in bioc.biostrings) tb_width (bioc.biostrings.TB_PDict attribute) term (bioc.annotationdbi.GOTerms attribute)

U

unaligned (bioc.biostrings.AlignedXStringSet0 attribute) union() (bioc.gseabase.GeneSet method) unmasked (bioc.biostrings.MaskedXString attribute)

urls (bioc.gseabase.GeneSet attribute)

V

Versioned (class in bioc.biobase) VersionedBiobase (class in bioc.biobase)

Views (class in bioc.iranges)

W

which() (bioc.biostrings.PDict method) whichfirst_notnormal() (bioc.iranges.Ranges method) width (bioc.biostrings.AlignedXStringSet0 attribute) (bioc.biostrings.PDict attribute) (bioc.biostrings.XStringViews attribute) (bioc.iranges.RangedData attribute) (bioc.iranges.Ranges attribute) (bioc.shortread.QualityScore attribute) (bioc.shortread.ShortRead attribute)

X

XDataFrameList (class in bioc.iranges) XRanges (class in bioc.iranges) XString (class in bioc.biostrings) XStringQuality (class in bioc.biostrings)

XStringSet (class in bioc.biostrings) XStringViews (class in bioc.biostrings)