bioinformatics-toolkit-0.4.1: A collection of bioinformatics tools

Index

&Bio.RealWorld.ENCODE
addTermBio.GO
AlignFnBio.Motif.Alignment
alignmentBio.Motif.Alignment
alignmentByBio.Motif.Alignment
alphabetBio.Seq
asBio.RealWorld.ENCODE
asBedBio.Data.Bed
assayIsBio.RealWorld.ENCODE
AssocRuleBio.GO.GREAT
BamBio.Data.Bam
bamToBedBio.Data.Bam
BasalPlusExtensionBio.GO.GREAT
BasicBio.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
BEDLikeBio.Data.Bed
bedNameBio.Data.Bed
bedScoreBio.Data.Bed
bedSizeBio.Data.Bed
bedStrandBio.Data.Bed
bedToTreeBio.Data.Bed
BEDTreeBio.Data.Bed
BGBio.Motif
binarySearchBio.Utils.Functions
binarySearchByBio.Utils.Functions
binarySearchByBoundsBio.Utils.Functions
binBySizeBio.Utils.Misc
binBySizeLeftBio.Utils.Misc
binBySizeOverlapBio.Utils.Misc
binsBio.Utils.Misc
BioIDBio.RealWorld.ID
BioSeqBio.Seq
BioSeq'Bio.Seq
BkgdBio.Motif
buildTreeBio.Motif.Merge
CDF 
1 (Type/Class)Bio.Motif
2 (Data Constructor)Bio.Motif
cdfBio.Motif
cdf'Bio.Motif
cellIsBio.RealWorld.ENCODE
chromBio.Data.Bed
chromEndBio.Data.Bed
chromStartBio.Data.Bed
closeGenomeBio.Seq.IO
CombineFnBio.Motif.Alignment
compareBedBio.Data.Bed
convertBio.Data.Bed
countTagsBinBedBio.ChIPSeq
countTagsBinBed'Bio.ChIPSeq
coverageBio.Utils.Overlap
cubPenalBio.Motif.Alignment
cutTreeByBio.Motif.Merge
defaultAssocRuleBio.GO.GREAT
diluteBio.Motif.Merge
DNABio.Seq
EncodeAcc 
1 (Type/Class)Bio.RealWorld.ID
2 (Data Constructor)Bio.RealWorld.ID
enrichmentBio.GO
EnsemblID 
1 (Type/Class)Bio.RealWorld.ID
2 (Data Constructor)Bio.RealWorld.ID
expPenalBio.Motif.Alignment
ExtBio.Seq
FastaLikeBio.Data.Fasta
fastaReaderBio.Data.Fasta
fetchByGeneNamesBio.RealWorld.BioGRID
fetchSeqBio.Data.Bed
fetchSeq'Bio.Data.Bed
filterFDRBio.Utils.Functions
findTFBSBio.Motif.Search
findTFBS'Bio.Motif.Search
findTFBSSlowBio.Motif.Search
fragLengthBio.ChIPSeq.FragLen
fromBSBio.Seq
fromFastaRecordBio.Data.Fasta
fromIDBio.RealWorld.ID
fromLineBio.Data.Bed
fromMEMEBio.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
gafAnnotationExtensionBio.GO.Parser
gafAspectBio.GO.Parser
gafAssignedByBio.GO.Parser
gafDateBio.GO.Parser
gafDbBio.GO.Parser
gafDbIdBio.GO.Parser
gafDbRefBio.GO.Parser
gafEvidenceCodeBio.GO.Parser
gafGeneProductIDBio.GO.Parser
gafGoIdBio.GO.Parser
gafNameBio.GO.Parser
gafQualifierBio.GO.Parser
gafSymbolBio.GO.Parser
gafSynonymBio.GO.Parser
gafTaxonBio.GO.Parser
gafTypeBio.GO.Parser
gafWithOrFromBio.GO.Parser
gcContentBio.Seq
gcContentPWMBio.Motif
Gene 
1 (Type/Class)Bio.RealWorld.GENCODE
2 (Data Constructor)Bio.RealWorld.GENCODE
geneChromBio.RealWorld.GENCODE
geneEndBio.RealWorld.GENCODE
geneIdBio.RealWorld.GENCODE
geneNameBio.RealWorld.GENCODE
geneStartBio.RealWorld.GENCODE
geneStrandBio.RealWorld.GENCODE
GenomeBio.Seq.IO
get3DRegulatoryDomainsBio.GO.GREAT
getChromBio.Seq.IO
getChrSizesBio.Seq.IO
getFileBio.RealWorld.ENCODE
getJunctionBio.RealWorld.UCSC
getMotifPValueBio.Data.Bed
getMotifScoreBio.Data.Bed
getParentByIdBio.GO
getRegulatoryDomainsBio.GO.GREAT
getSeqBio.Seq.IO
getTSSBio.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
GOIdBio.GO
GOMapBio.GO
HeaderStateBio.Data.Bam
hReadBedBio.Data.Bed
hReadBed'Bio.Data.Bed
hWriteBedBio.Data.Bed
hWriteBed'Bio.Data.Bed
hyperquickBio.Utils.Functions
icBio.Motif
ihsBio.Utils.Functions
ihs'Bio.Utils.Functions
intersectBedBio.Data.Bed
intersectBedWithBio.Data.Bed
intersectingBio.Data.Bed
intersectSortedBedBio.Data.Bed
intersectSortedBedWithBio.Data.Bed
isIntersectedBio.Data.Bed
isOverlappedBio.Data.Bed
iterativeMergeBio.Motif.Merge
IUPACBio.Seq
jsdBio.Utils.Functions
jsonFromUrlBio.RealWorld.ENCODE
KeyWords 
1 (Type/Class)Bio.RealWorld.ENCODE
2 (Data Constructor)Bio.RealWorld.ENCODE
kldBio.Utils.Functions
l1Bio.Motif.Alignment
l2Bio.Motif.Alignment
l3Bio.Motif.Alignment
lengthBio.Seq
lInfBio.Motif.Alignment
linPenalBio.Motif.Alignment
lookupBio.RealWorld.Ensembl
maxMatchScBio.Motif.Search
mergeBedBio.Data.Bed
mergeBedWithBio.Data.Bed
mergePWMBio.Motif.Merge
mergePWMWeightedBio.Motif.Merge
mergeSortedBedBio.Data.Bed
mergeSortedBedWithBio.Data.Bed
mergeTreeBio.Motif.Merge
mergeTreeWeightedBio.Motif.Merge
mkIndexBio.Seq.IO
monoColonalizeBio.ChIPSeq
Motif 
1 (Type/Class)Bio.Motif
2 (Data Constructor)Bio.Motif
motifScanBio.Data.Bed
naiveCCWithSmoothBio.ChIPSeq.FragLen
NarrowPeak 
1 (Type/Class)Bio.Data.Bed
2 (Data Constructor)Bio.Data.Bed
nucleotideFreqBio.Seq
OneNearestBio.GO.GREAT
openGenomeBio.Seq.IO
openUrlBio.RealWorld.ENCODE
optimalScoreBio.Motif
orderingBio.Utils.Types
organismIsBio.RealWorld.ENCODE
overlapFragmentBio.Utils.Overlap
overlapNuclBio.Utils.Overlap
parseGenesBio.RealWorld.GENCODE
peakClusterBio.ChIPSeq
PeptideBio.Seq
pValueToScoreBio.Motif
pValueToScoreExactBio.Motif
PWM 
1 (Type/Class)Bio.Motif
2 (Data Constructor)Bio.Motif
quadPenalBio.Motif.Alignment
quantileNormalizationBio.Utils.Functions
queryByIdBio.RealWorld.ENCODE
rcBio.Seq
rcPWMBio.Motif
read3DContactBio.GO.GREAT
readBamBio.Data.Bam
readBedBio.Data.Bed
readBed'Bio.Data.Bed
readDoubleBio.Utils.Misc
readFastaBio.Data.Fasta
readFasta'Bio.Data.Fasta
readGAFBio.GO.Parser
readGenesBio.RealWorld.GENCODE
readGenes'Bio.RealWorld.GENCODE
readIntBio.Utils.Misc
readMEMEBio.Motif
readOWLBio.GO.Parser
readOWLAsMapBio.GO.Parser
readUCSCGenesBio.RealWorld.UCSC
readUCSCGenes'Bio.RealWorld.UCSC
RNABio.Seq
rpkmBedBio.ChIPSeq
rpkmSortedBedBio.ChIPSeq
scaleBio.Utils.Functions
scoreBio.Motif
scoreCDFBio.Motif
scoresBio.Motif
scores'Bio.Motif
searchBio.RealWorld.ENCODE
showResultBio.RealWorld.ENCODE
sizeBio.Motif
sizeOverlappedBio.Data.Bed
sliceBio.Seq
slideAverageBio.Utils.Functions
sortBedBio.Data.Bed
Sorted 
1 (Type/Class)Bio.Data.Bed
2 (Data Constructor)Bio.Data.Bed
3 (Type/Class)Bio.Utils.Types
sortedBamToBedPEBio.Data.Bam
sortedBedToTreeBio.Data.Bed
spaceConstraintBio.Motif.Search
spaceConstraintHelperBio.Motif.Search
SpaceDistribution 
1 (Type/Class)Bio.Motif.Search
2 (Data Constructor)Bio.Motif.Search
splitBedBio.Data.Bed
splitBedBySizeBio.Data.Bed
splitBedBySizeLeftBio.Data.Bed
splitBedBySizeOverlapBio.Data.Bed
splitOverlappedBio.Data.Bed
subPWMBio.Motif
TAB2 
1 (Type/Class)Bio.RealWorld.BioGRID
2 (Data Constructor)Bio.RealWorld.BioGRID
tagCountDistrBio.ChIPSeq
termsBio.RealWorld.ENCODE
toBSBio.Seq
toIDBio.RealWorld.ID
toIUPACBio.Motif
toLineBio.Data.Bed
toMEMEBio.Motif
toPWMBio.Motif
toSortedBio.Utils.Types
trimBio.Motif.Merge
truncateCDFBio.Motif
TwoNearestBio.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
unsafeFromBSBio.Seq
unsafeToSortedBio.Utils.Types
withBamFileBio.Data.Bam
withGenomeBio.Seq.IO
writeBamBio.Data.Bam
writeBedBio.Data.Bed
writeBed'Bio.Data.Bed
writeFastaBio.Motif
writeMEMEBio.Motif
_alignIdBio.RealWorld.UCSC
_biogridIdBio.RealWorld.BioGRID
_biogridIdABio.RealWorld.BioGRID
_biogridIdBBio.RealWorld.BioGRID
_cdsBio.RealWorld.UCSC
_chrom 
1 (Function)Bio.RealWorld.UCSC
2 (Function)Bio.Data.Bed
_chromEndBio.Data.Bed
_chromStartBio.Data.Bed
_entrezIdABio.RealWorld.BioGRID
_entrezIdBBio.RealWorld.BioGRID
_exonsBio.RealWorld.UCSC
_experimentalSystemNameBio.RealWorld.BioGRID
_experimentalSystemTypeBio.RealWorld.BioGRID
_firstAuthorBio.RealWorld.BioGRID
_geneNameBio.RealWorld.UCSC
_intronsBio.RealWorld.UCSC
_labelBio.GO
_matBio.Motif
_motif1Bio.Motif.Search
_motif2Bio.Motif.Search
_name 
1 (Function)Bio.Motif
2 (Function)Bio.Data.Bed
_npChromBio.Data.Bed
_npEndBio.Data.Bed
_npNameBio.Data.Bed
_npPeakBio.Data.Bed
_npPvalueBio.Data.Bed
_npQvalueBio.Data.Bed
_npScoreBio.Data.Bed
_npSigalBio.Data.Bed
_npStartBio.Data.Bed
_npStrandBio.Data.Bed
_nSitesBio.Motif
_nSites1Bio.Motif.Search
_nSites2Bio.Motif.Search
_oboIdBio.GO
_oboNSBio.GO
_oppositeBio.Motif.Search
_organismIdABio.RealWorld.BioGRID
_organismIdBBio.RealWorld.BioGRID
_phenotypesBio.RealWorld.BioGRID
_proteinIdBio.RealWorld.UCSC
_ptmBio.RealWorld.BioGRID
_pubmedIdBio.RealWorld.BioGRID
_pwmBio.Motif
_qualificationsBio.RealWorld.BioGRID
_sameBio.Motif.Search
_score 
1 (Function)Bio.RealWorld.BioGRID
2 (Function)Bio.Data.Bed
_sourceBio.RealWorld.BioGRID
_strand 
1 (Function)Bio.RealWorld.UCSC
2 (Function)Bio.Data.Bed
_subProcessOfBio.GO
_symbolABio.RealWorld.BioGRID
_symbolBBio.RealWorld.BioGRID
_synonymsABio.RealWorld.BioGRID
_synonymsBBio.RealWorld.BioGRID
_systematicNameABio.RealWorld.BioGRID
_systematicNameBBio.RealWorld.BioGRID
_tagsBio.RealWorld.BioGRID
_throughputBio.RealWorld.BioGRID
_transcriptBio.RealWorld.UCSC
|!Bio.RealWorld.ENCODE
|@Bio.RealWorld.ENCODE