! | Bio.Utils.BitVector |
& | 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.Types, Bio.Data.Bed |
assayIs | Bio.RealWorld.ENCODE |
BAM | Bio.Data.Bam |
bamToBed | Bio.Data.Bam |
bamToBedC | Bio.Data.Bam |
bamToFastq | Bio.Data.Bam |
bamToFastqC | Bio.Data.Bam |
BaseMap | |
1 (Type/Class) | Bio.Data.Bed.Utils |
2 (Data Constructor) | Bio.Data.Bed.Utils |
baseMap | Bio.Data.Bed.Utils |
Basic | Bio.Seq |
BED | |
1 (Type/Class) | Bio.Data.Bed.Types, Bio.Data.Bed |
2 (Data Constructor) | Bio.Data.Bed.Types |
BED3 | |
1 (Type/Class) | Bio.Data.Bed.Types, Bio.Data.Bed |
2 (Data Constructor) | Bio.Data.Bed.Types |
BEDConvert | Bio.Data.Bed.Types, Bio.Data.Bed |
BEDExt | |
1 (Type/Class) | Bio.Data.Bed.Types, Bio.Data.Bed |
2 (Data Constructor) | Bio.Data.Bed.Types, Bio.Data.Bed |
BEDLike | Bio.Data.Bed.Types, Bio.Data.Bed |
bedToTree | Bio.Data.Bed |
BEDTree | Bio.Data.Bed.Types, 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 |
BitMVector | Bio.Utils.BitVector |
BitVector | |
1 (Type/Class) | Bio.Utils.BitVector |
2 (Data Constructor) | Bio.Utils.BitVector |
Bkgd | Bio.Motif |
bpPvalue | Bio.Data.Bed.Types |
bpQvalue | Bio.Data.Bed.Types |
bpSignal | Bio.Data.Bed.Types |
BroadPeak | |
1 (Type/Class) | Bio.Data.Bed.Types |
2 (Data Constructor) | Bio.Data.Bed.Types |
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.Types, Bio.Data.Bed |
chromEnd | Bio.Data.Bed.Types, Bio.Data.Bed |
chromStart | Bio.Data.Bed.Types, Bio.Data.Bed |
clear | Bio.Utils.BitVector |
closeGenome | Bio.Seq.IO |
CombineFn | Bio.Motif.Alignment |
compareBed | Bio.Data.Bed |
convert | Bio.Data.Bed.Types, Bio.Data.Bed |
countTagsBinBed | Bio.Data.Bed.Utils |
countTagsBinBed' | Bio.Data.Bed.Utils |
coverage | Bio.Utils.Overlap |
cubPenal | Bio.Motif.Alignment |
cutTreeBy | Bio.Motif.Merge |
dilute | Bio.Motif.Merge |
DNA | Bio.Seq |
downloadData | Bio.RealWorld.GDC |
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 |
Fastq | |
1 (Type/Class) | Bio.Data.Fastq |
2 (Data Constructor) | Bio.Data.Fastq |
fastqSeq | Bio.Data.Fastq |
fastqSeqId | Bio.Data.Fastq |
fastqSeqQual | Bio.Data.Fastq |
fastqToByteString | Bio.Data.Fastq |
fetchByGeneNames | Bio.RealWorld.BioGRID |
fetchSeq | Bio.Data.Bed.Utils |
fetchSeq' | Bio.Data.Bed.Utils |
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.Types, Bio.Data.Bed |
fromMEME | Bio.Motif |
fromSorted | |
1 (Function) | Bio.Data.Bed.Types |
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 |
geneExon | Bio.RealWorld.GENCODE |
geneId | Bio.RealWorld.GENCODE |
geneLeft | Bio.RealWorld.GENCODE |
geneName | Bio.RealWorld.GENCODE |
geneRight | Bio.RealWorld.GENCODE |
geneStrand | Bio.RealWorld.GENCODE |
geneTranscripts | Bio.RealWorld.GENCODE |
Genome | Bio.Seq.IO |
getBamHeader | Bio.Data.Bam |
getChrom | Bio.Seq.IO |
getChrSizes | Bio.Seq.IO |
getFile | Bio.RealWorld.ENCODE |
getJunction | Bio.RealWorld.UCSC |
getMotifPValue | Bio.Data.Bed.Utils |
getMotifScore | Bio.Data.Bed.Utils |
getParentById | Bio.GO |
getPathways | Bio.RealWorld.Reactome |
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 |
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 |
mapID | Bio.RealWorld.Uniprot |
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.Data.Bed.Utils |
Motif | |
1 (Type/Class) | Bio.Motif |
2 (Data Constructor) | Bio.Motif |
motifScan | Bio.Data.Bed.Utils |
naiveCCWithSmooth | Bio.ChIPSeq.FragLen |
name | Bio.Data.Bed.Types, Bio.Data.Bed |
NarrowPeak | |
1 (Type/Class) | Bio.Data.Bed.Types, Bio.Data.Bed |
2 (Data Constructor) | Bio.Data.Bed.Types |
npPeak | Bio.Data.Bed.Types, Bio.Data.Bed |
npPvalue | Bio.Data.Bed.Types, Bio.Data.Bed |
npQvalue | Bio.Data.Bed.Types, Bio.Data.Bed |
npSignal | Bio.Data.Bed.Types, Bio.Data.Bed |
nucleotideFreq | Bio.Seq |
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 |
parseFastqC | Bio.Data.Fastq |
peakCluster | Bio.Data.Bed.Utils |
Peptide | Bio.Seq |
pValueToScore | Bio.Motif |
pValueToScoreExact | Bio.Motif |
PWM | |
1 (Type/Class) | Bio.Motif |
2 (Data Constructor) | Bio.Motif |
quadPenal | Bio.Motif.Alignment |
qualitySummary | Bio.Data.Fastq |
quantileNormalization | Bio.Utils.Functions |
queryBaseMap | Bio.Data.Bed.Utils |
queryById | Bio.RealWorld.ENCODE |
rc | Bio.Seq |
rcPWM | Bio.Motif |
readBed | Bio.Data.Bed |
readDouble | Bio.Utils.Misc |
readFasta | Bio.Data.Fasta |
readFasta' | Bio.Data.Fasta |
readGAF | Bio.GO.Parser |
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.Data.Bed.Utils |
rpkmSortedBed | Bio.Data.Bed.Utils |
scale | Bio.Utils.Functions |
score | |
1 (Function) | Bio.Motif |
2 (Function) | Bio.Data.Bed.Types, Bio.Data.Bed |
scoreCDF | Bio.Motif |
scores | Bio.Motif |
scores' | Bio.Motif |
search | Bio.RealWorld.ENCODE |
set | Bio.Utils.BitVector |
showResult | Bio.RealWorld.ENCODE |
sinkBam | Bio.Data.Bam |
sinkFastq | Bio.Data.Fastq |
sinkFastqGzip | Bio.Data.Fastq |
sinkFileBed | Bio.Data.Bed |
sinkFileBedGzip | Bio.Data.Bed |
sinkHandleBed | Bio.Data.Bed |
size | |
1 (Function) | Bio.Utils.BitVector |
2 (Function) | Bio.Motif |
3 (Function) | Bio.Data.Bed.Types, Bio.Data.Bed |
sizeOverlapped | Bio.Data.Bed |
slice | Bio.Seq |
slideAverage | Bio.Utils.Functions |
sortBed | Bio.Data.Bed |
Sorted | |
1 (Type/Class) | Bio.Data.Bed.Types |
2 (Data Constructor) | Bio.Data.Bed.Types |
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 |
strand | Bio.Data.Bed.Types, Bio.Data.Bed |
streamBam | Bio.Data.Bam |
streamBed | Bio.Data.Bed |
streamBedGzip | Bio.Data.Bed |
streamElements | Bio.RealWorld.GENCODE |
streamFastq | Bio.Data.Fastq |
streamFastqGzip | Bio.Data.Fastq |
subPWM | Bio.Motif |
TAB2 | |
1 (Type/Class) | Bio.RealWorld.BioGRID |
2 (Data Constructor) | Bio.RealWorld.BioGRID |
tagCountDistr | Bio.Data.Bed.Utils |
terms | Bio.RealWorld.ENCODE |
toBS | Bio.Seq |
toID | Bio.RealWorld.ID |
toIUPAC | Bio.Motif |
toLine | Bio.Data.Bed.Types, Bio.Data.Bed |
toList | Bio.Utils.BitVector |
toMEME | Bio.Motif |
toPWM | Bio.Motif |
toSorted | Bio.Utils.Types |
trim | Bio.Motif.Merge |
trimPolyA | Bio.Data.Fastq |
truncateCDF | Bio.Motif |
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 |
unsafeFreeze | Bio.Utils.BitVector |
unsafeFromBS | Bio.Seq |
unsafeToSorted | Bio.Utils.Types |
withGenome | Bio.Seq.IO |
writeBed | Bio.Data.Bed |
writeFasta | Bio.Motif |
writeMEME | Bio.Motif |
zeros | Bio.Utils.BitVector |
_alignId | Bio.RealWorld.UCSC |
_bed | Bio.Data.Bed.Types, Bio.Data.Bed |
_bed3_chrom | Bio.Data.Bed.Types |
_bed3_chrom_end | Bio.Data.Bed.Types |
_bed3_chrom_start | Bio.Data.Bed.Types |
_bed_chrom | Bio.Data.Bed.Types |
_bed_chromEnd | Bio.Data.Bed.Types |
_bed_chromStart | Bio.Data.Bed.Types |
_bed_name | Bio.Data.Bed.Types |
_bed_score | Bio.Data.Bed.Types |
_bed_strand | Bio.Data.Bed.Types |
_biogridId | Bio.RealWorld.BioGRID |
_biogridIdA | Bio.RealWorld.BioGRID |
_biogridIdB | Bio.RealWorld.BioGRID |
_bpChrom | Bio.Data.Bed.Types |
_bpEnd | Bio.Data.Bed.Types |
_bpName | Bio.Data.Bed.Types |
_bpPvalue | Bio.Data.Bed.Types |
_bpQvalue | Bio.Data.Bed.Types |
_bpScore | Bio.Data.Bed.Types |
_bpSignal | Bio.Data.Bed.Types |
_bpStart | Bio.Data.Bed.Types |
_bpStrand | Bio.Data.Bed.Types |
_cds | Bio.RealWorld.UCSC |
_chrom | Bio.RealWorld.UCSC |
_data | Bio.Data.Bed.Types, Bio.Data.Bed |
_entrezIdA | Bio.RealWorld.BioGRID |
_entrezIdB | Bio.RealWorld.BioGRID |
_exons | Bio.RealWorld.UCSC |
_experimentalSystemName | Bio.RealWorld.BioGRID |
_experimentalSystemType | Bio.RealWorld.BioGRID |
_ext_bed | Bio.Data.Bed.Types, Bio.Data.Bed |
_ext_data | Bio.Data.Bed.Types, Bio.Data.Bed |
_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 | Bio.Motif |
_npChrom | Bio.Data.Bed.Types |
_npEnd | Bio.Data.Bed.Types |
_npName | Bio.Data.Bed.Types |
_npPeak | Bio.Data.Bed.Types |
_npPvalue | Bio.Data.Bed.Types |
_npQvalue | Bio.Data.Bed.Types |
_npScore | Bio.Data.Bed.Types |
_npSignal | Bio.Data.Bed.Types |
_npStart | Bio.Data.Bed.Types |
_npStrand | Bio.Data.Bed.Types |
_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 | Bio.RealWorld.BioGRID |
_source | Bio.RealWorld.BioGRID |
_strand | Bio.RealWorld.UCSC |
_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 |
|! | Bio.RealWorld.ENCODE |
|@ | Bio.RealWorld.ENCODE |