Contents
Index
bioinformatics-toolkit-0.4.1: A collection of bioinformatics tools
Index
&
Bio.RealWorld.ENCODE
addTerm
Bio.GO
AlignFn
Bio.Motif.Alignment
alignment
Bio.Motif.Alignment
alignmentBy
Bio.Motif.Alignment
alphabet
Bio.Seq
as
Bio.RealWorld.ENCODE
asBed
Bio.Data.Bed
assayIs
Bio.RealWorld.ENCODE
AssocRule
Bio.GO.GREAT
Bam
Bio.Data.Bam
bamToBed
Bio.Data.Bam
BasalPlusExtension
Bio.GO.GREAT
Basic
Bio.Seq
BED
1 (Type/Class)
Bio.Data.Bed
2 (Data Constructor)
Bio.Data.Bed
BED3
1 (Type/Class)
Bio.Data.Bed
2 (Data Constructor)
Bio.Data.Bed
BEDLike
Bio.Data.Bed
bedName
Bio.Data.Bed
bedScore
Bio.Data.Bed
bedSize
Bio.Data.Bed
bedStrand
Bio.Data.Bed
bedToTree
Bio.Data.Bed
BEDTree
Bio.Data.Bed
BG
Bio.Motif
binarySearch
Bio.Utils.Functions
binarySearchBy
Bio.Utils.Functions
binarySearchByBounds
Bio.Utils.Functions
binBySize
Bio.Utils.Misc
binBySizeLeft
Bio.Utils.Misc
binBySizeOverlap
Bio.Utils.Misc
bins
Bio.Utils.Misc
BioID
Bio.RealWorld.ID
BioSeq
Bio.Seq
BioSeq'
Bio.Seq
Bkgd
Bio.Motif
buildTree
Bio.Motif.Merge
CDF
1 (Type/Class)
Bio.Motif
2 (Data Constructor)
Bio.Motif
cdf
Bio.Motif
cdf'
Bio.Motif
cellIs
Bio.RealWorld.ENCODE
chrom
Bio.Data.Bed
chromEnd
Bio.Data.Bed
chromStart
Bio.Data.Bed
closeGenome
Bio.Seq.IO
CombineFn
Bio.Motif.Alignment
compareBed
Bio.Data.Bed
convert
Bio.Data.Bed
countTagsBinBed
Bio.ChIPSeq
countTagsBinBed'
Bio.ChIPSeq
coverage
Bio.Utils.Overlap
cubPenal
Bio.Motif.Alignment
cutTreeBy
Bio.Motif.Merge
defaultAssocRule
Bio.GO.GREAT
dilute
Bio.Motif.Merge
DNA
Bio.Seq
EncodeAcc
1 (Type/Class)
Bio.RealWorld.ID
2 (Data Constructor)
Bio.RealWorld.ID
enrichment
Bio.GO
EnsemblID
1 (Type/Class)
Bio.RealWorld.ID
2 (Data Constructor)
Bio.RealWorld.ID
expPenal
Bio.Motif.Alignment
Ext
Bio.Seq
FastaLike
Bio.Data.Fasta
fastaReader
Bio.Data.Fasta
fetchByGeneNames
Bio.RealWorld.BioGRID
fetchSeq
Bio.Data.Bed
fetchSeq'
Bio.Data.Bed
filterFDR
Bio.Utils.Functions
findTFBS
Bio.Motif.Search
findTFBS'
Bio.Motif.Search
findTFBSSlow
Bio.Motif.Search
fragLength
Bio.ChIPSeq.FragLen
fromBS
Bio.Seq
fromFastaRecord
Bio.Data.Fasta
fromID
Bio.RealWorld.ID
fromLine
Bio.Data.Bed
fromMEME
Bio.Motif
fromSorted
1 (Function)
Bio.Data.Bed
2 (Function)
Bio.Utils.Types
GAF
1 (Type/Class)
Bio.GO.Parser
2 (Data Constructor)
Bio.GO.Parser
gafAnnotationExtension
Bio.GO.Parser
gafAspect
Bio.GO.Parser
gafAssignedBy
Bio.GO.Parser
gafDate
Bio.GO.Parser
gafDb
Bio.GO.Parser
gafDbId
Bio.GO.Parser
gafDbRef
Bio.GO.Parser
gafEvidenceCode
Bio.GO.Parser
gafGeneProductID
Bio.GO.Parser
gafGoId
Bio.GO.Parser
gafName
Bio.GO.Parser
gafQualifier
Bio.GO.Parser
gafSymbol
Bio.GO.Parser
gafSynonym
Bio.GO.Parser
gafTaxon
Bio.GO.Parser
gafType
Bio.GO.Parser
gafWithOrFrom
Bio.GO.Parser
gcContent
Bio.Seq
gcContentPWM
Bio.Motif
Gene
1 (Type/Class)
Bio.RealWorld.GENCODE
2 (Data Constructor)
Bio.RealWorld.GENCODE
geneChrom
Bio.RealWorld.GENCODE
geneEnd
Bio.RealWorld.GENCODE
geneId
Bio.RealWorld.GENCODE
geneName
Bio.RealWorld.GENCODE
geneStart
Bio.RealWorld.GENCODE
geneStrand
Bio.RealWorld.GENCODE
Genome
Bio.Seq.IO
get3DRegulatoryDomains
Bio.GO.GREAT
getChrom
Bio.Seq.IO
getChrSizes
Bio.Seq.IO
getFile
Bio.RealWorld.ENCODE
getJunction
Bio.RealWorld.UCSC
getMotifPValue
Bio.Data.Bed
getMotifScore
Bio.Data.Bed
getParentById
Bio.GO
getRegulatoryDomains
Bio.GO.GREAT
getSeq
Bio.Seq.IO
getTSS
Bio.RealWorld.UCSC
GO
1 (Type/Class)
Bio.GO
2 (Data Constructor)
Bio.GO
GOID
1 (Type/Class)
Bio.RealWorld.ID
2 (Data Constructor)
Bio.RealWorld.ID
GOId
Bio.GO
GOMap
Bio.GO
HeaderState
Bio.Data.Bam
hReadBed
Bio.Data.Bed
hReadBed'
Bio.Data.Bed
hWriteBed
Bio.Data.Bed
hWriteBed'
Bio.Data.Bed
hyperquick
Bio.Utils.Functions
ic
Bio.Motif
ihs
Bio.Utils.Functions
ihs'
Bio.Utils.Functions
intersectBed
Bio.Data.Bed
intersectBedWith
Bio.Data.Bed
intersecting
Bio.Data.Bed
intersectSortedBed
Bio.Data.Bed
intersectSortedBedWith
Bio.Data.Bed
isIntersected
Bio.Data.Bed
isOverlapped
Bio.Data.Bed
iterativeMerge
Bio.Motif.Merge
IUPAC
Bio.Seq
jsd
Bio.Utils.Functions
jsonFromUrl
Bio.RealWorld.ENCODE
KeyWords
1 (Type/Class)
Bio.RealWorld.ENCODE
2 (Data Constructor)
Bio.RealWorld.ENCODE
kld
Bio.Utils.Functions
l1
Bio.Motif.Alignment
l2
Bio.Motif.Alignment
l3
Bio.Motif.Alignment
length
Bio.Seq
lInf
Bio.Motif.Alignment
linPenal
Bio.Motif.Alignment
lookup
Bio.RealWorld.Ensembl
maxMatchSc
Bio.Motif.Search
mergeBed
Bio.Data.Bed
mergeBedWith
Bio.Data.Bed
mergePWM
Bio.Motif.Merge
mergePWMWeighted
Bio.Motif.Merge
mergeSortedBed
Bio.Data.Bed
mergeSortedBedWith
Bio.Data.Bed
mergeTree
Bio.Motif.Merge
mergeTreeWeighted
Bio.Motif.Merge
mkIndex
Bio.Seq.IO
monoColonalize
Bio.ChIPSeq
Motif
1 (Type/Class)
Bio.Motif
2 (Data Constructor)
Bio.Motif
motifScan
Bio.Data.Bed
naiveCCWithSmooth
Bio.ChIPSeq.FragLen
NarrowPeak
1 (Type/Class)
Bio.Data.Bed
2 (Data Constructor)
Bio.Data.Bed
nucleotideFreq
Bio.Seq
OneNearest
Bio.GO.GREAT
openGenome
Bio.Seq.IO
openUrl
Bio.RealWorld.ENCODE
optimalScore
Bio.Motif
ordering
Bio.Utils.Types
organismIs
Bio.RealWorld.ENCODE
overlapFragment
Bio.Utils.Overlap
overlapNucl
Bio.Utils.Overlap
parseGenes
Bio.RealWorld.GENCODE
peakCluster
Bio.ChIPSeq
Peptide
Bio.Seq
pValueToScore
Bio.Motif
pValueToScoreExact
Bio.Motif
PWM
1 (Type/Class)
Bio.Motif
2 (Data Constructor)
Bio.Motif
quadPenal
Bio.Motif.Alignment
quantileNormalization
Bio.Utils.Functions
queryById
Bio.RealWorld.ENCODE
rc
Bio.Seq
rcPWM
Bio.Motif
read3DContact
Bio.GO.GREAT
readBam
Bio.Data.Bam
readBed
Bio.Data.Bed
readBed'
Bio.Data.Bed
readDouble
Bio.Utils.Misc
readFasta
Bio.Data.Fasta
readFasta'
Bio.Data.Fasta
readGAF
Bio.GO.Parser
readGenes
Bio.RealWorld.GENCODE
readGenes'
Bio.RealWorld.GENCODE
readInt
Bio.Utils.Misc
readMEME
Bio.Motif
readOWL
Bio.GO.Parser
readOWLAsMap
Bio.GO.Parser
readUCSCGenes
Bio.RealWorld.UCSC
readUCSCGenes'
Bio.RealWorld.UCSC
RNA
Bio.Seq
rpkmBed
Bio.ChIPSeq
rpkmSortedBed
Bio.ChIPSeq
scale
Bio.Utils.Functions
score
Bio.Motif
scoreCDF
Bio.Motif
scores
Bio.Motif
scores'
Bio.Motif
search
Bio.RealWorld.ENCODE
showResult
Bio.RealWorld.ENCODE
size
Bio.Motif
sizeOverlapped
Bio.Data.Bed
slice
Bio.Seq
slideAverage
Bio.Utils.Functions
sortBed
Bio.Data.Bed
Sorted
1 (Type/Class)
Bio.Data.Bed
2 (Data Constructor)
Bio.Data.Bed
3 (Type/Class)
Bio.Utils.Types
sortedBamToBedPE
Bio.Data.Bam
sortedBedToTree
Bio.Data.Bed
spaceConstraint
Bio.Motif.Search
spaceConstraintHelper
Bio.Motif.Search
SpaceDistribution
1 (Type/Class)
Bio.Motif.Search
2 (Data Constructor)
Bio.Motif.Search
splitBed
Bio.Data.Bed
splitBedBySize
Bio.Data.Bed
splitBedBySizeLeft
Bio.Data.Bed
splitBedBySizeOverlap
Bio.Data.Bed
splitOverlapped
Bio.Data.Bed
subPWM
Bio.Motif
TAB2
1 (Type/Class)
Bio.RealWorld.BioGRID
2 (Data Constructor)
Bio.RealWorld.BioGRID
tagCountDistr
Bio.ChIPSeq
terms
Bio.RealWorld.ENCODE
toBS
Bio.Seq
toID
Bio.RealWorld.ID
toIUPAC
Bio.Motif
toLine
Bio.Data.Bed
toMEME
Bio.Motif
toPWM
Bio.Motif
toSorted
Bio.Utils.Types
trim
Bio.Motif.Merge
truncateCDF
Bio.Motif
TwoNearest
Bio.GO.GREAT
UCSCGene
1 (Type/Class)
Bio.RealWorld.UCSC
2 (Data Constructor)
Bio.RealWorld.UCSC
UCSCID
1 (Type/Class)
Bio.RealWorld.ID
2 (Data Constructor)
Bio.RealWorld.ID
UniprotID
1 (Type/Class)
Bio.RealWorld.ID
2 (Data Constructor)
Bio.RealWorld.ID
unsafeFromBS
Bio.Seq
unsafeToSorted
Bio.Utils.Types
withBamFile
Bio.Data.Bam
withGenome
Bio.Seq.IO
writeBam
Bio.Data.Bam
writeBed
Bio.Data.Bed
writeBed'
Bio.Data.Bed
writeFasta
Bio.Motif
writeMEME
Bio.Motif
_alignId
Bio.RealWorld.UCSC
_biogridId
Bio.RealWorld.BioGRID
_biogridIdA
Bio.RealWorld.BioGRID
_biogridIdB
Bio.RealWorld.BioGRID
_cds
Bio.RealWorld.UCSC
_chrom
1 (Function)
Bio.RealWorld.UCSC
2 (Function)
Bio.Data.Bed
_chromEnd
Bio.Data.Bed
_chromStart
Bio.Data.Bed
_entrezIdA
Bio.RealWorld.BioGRID
_entrezIdB
Bio.RealWorld.BioGRID
_exons
Bio.RealWorld.UCSC
_experimentalSystemName
Bio.RealWorld.BioGRID
_experimentalSystemType
Bio.RealWorld.BioGRID
_firstAuthor
Bio.RealWorld.BioGRID
_geneName
Bio.RealWorld.UCSC
_introns
Bio.RealWorld.UCSC
_label
Bio.GO
_mat
Bio.Motif
_motif1
Bio.Motif.Search
_motif2
Bio.Motif.Search
_name
1 (Function)
Bio.Motif
2 (Function)
Bio.Data.Bed
_npChrom
Bio.Data.Bed
_npEnd
Bio.Data.Bed
_npName
Bio.Data.Bed
_npPeak
Bio.Data.Bed
_npPvalue
Bio.Data.Bed
_npQvalue
Bio.Data.Bed
_npScore
Bio.Data.Bed
_npSigal
Bio.Data.Bed
_npStart
Bio.Data.Bed
_npStrand
Bio.Data.Bed
_nSites
Bio.Motif
_nSites1
Bio.Motif.Search
_nSites2
Bio.Motif.Search
_oboId
Bio.GO
_oboNS
Bio.GO
_opposite
Bio.Motif.Search
_organismIdA
Bio.RealWorld.BioGRID
_organismIdB
Bio.RealWorld.BioGRID
_phenotypes
Bio.RealWorld.BioGRID
_proteinId
Bio.RealWorld.UCSC
_ptm
Bio.RealWorld.BioGRID
_pubmedId
Bio.RealWorld.BioGRID
_pwm
Bio.Motif
_qualifications
Bio.RealWorld.BioGRID
_same
Bio.Motif.Search
_score
1 (Function)
Bio.RealWorld.BioGRID
2 (Function)
Bio.Data.Bed
_source
Bio.RealWorld.BioGRID
_strand
1 (Function)
Bio.RealWorld.UCSC
2 (Function)
Bio.Data.Bed
_subProcessOf
Bio.GO
_symbolA
Bio.RealWorld.BioGRID
_symbolB
Bio.RealWorld.BioGRID
_synonymsA
Bio.RealWorld.BioGRID
_synonymsB
Bio.RealWorld.BioGRID
_systematicNameA
Bio.RealWorld.BioGRID
_systematicNameB
Bio.RealWorld.BioGRID
_tags
Bio.RealWorld.BioGRID
_throughput
Bio.RealWorld.BioGRID
_transcript
Bio.RealWorld.UCSC
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Bio.RealWorld.ENCODE
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Bio.RealWorld.ENCODE