Index

A

align() (tadlib.hitad.aligner.DomainAligner method) (tadlib.hitad.aligner.SingleBound method) (tadlib.hitad.aligner.SingleDomain method)

all_in_one() (tadlib.hitad.aligner.BoundAligner method)

B

BoundAligner (class in tadlib.hitad.aligner)

BoundSet (class in tadlib.hitad.aligner)

C

calarea() (tadlib.calfea.polygon.Polygon method) calDI() (tadlib.hitad.chromLev.Chrom method) callDomain() (tadlib.hitad.chromLev.Chrom method) (tadlib.hitad.chromLev.MultiReps method) callHierDomain() (tadlib.hitad.genomeLev.Genome method) Chrom (class in tadlib.hitad.chromLev) close() (tadlib.calfea.polygon.Polygon method)

collinear() (in module tadlib.calfea.polygon) conserved() (tadlib.hitad.aligner.DomainAligner method) conserved_sub_bounds() (tadlib.hitad.aligner.BoundAligner method) conserved_tad_bounds() (tadlib.hitad.aligner.BoundAligner method) Container (class in tadlib.hitad.aligner) convertMatrix() (tadlib.calfea.analyze.Core method) Core (class in tadlib.calfea.analyze)

D

DBSCAN() (tadlib.calfea.analyze.Core method) detectPeaks() (tadlib.hitad.chromLev.Chrom method) disappeared_sub() (tadlib.hitad.aligner.BoundAligner method)

disappeared_tad() (tadlib.hitad.aligner.BoundAligner method) DomainAligner (class in tadlib.hitad.aligner) DomainSet (class in tadlib.hitad.aligner)

F

fineDomain() (tadlib.hitad.chromLev.Chrom method)

G

gdensity() (tadlib.calfea.analyze.Core method) genDomainTree() (tadlib.hitad.aligner.DomainSet method) Genome (class in tadlib.hitad.genomeLev) getBottoms() (tadlib.hitad.aligner.DomainSet method)

getDomainList() (tadlib.hitad.chromLev.Chrom method) (tadlib.hitad.chromLev.MultiReps method) getregion() (tadlib.hitad.aligner.DomainSet method) getSelfMatrix() (tadlib.hitad.chromLev.Chrom method) getWeightMatrix() (tadlib.hitad.chromLev.Chrom method)

H

hierFormat() (in module tadlib.hitad.aligner)

I

idxmatch() (tadlib.hitad.chromLev.Chrom method) inner_changed() (tadlib.hitad.aligner.DomainAligner method)

isinside() (tadlib.calfea.polygon.Polygon method) iterCore() (tadlib.hitad.chromLev.Chrom method)

L

learning() (tadlib.hitad.genomeLev.Genome method)

load_TAD() (in module tadlib.calfea.analyze) longrange() (tadlib.calfea.analyze.Core method)

M

manipulation() (in module tadlib.calfea.analyze) maxCore() (tadlib.hitad.chromLev.Chrom method) maxscorepath() (tadlib.hitad.chromLev.Chrom method)

merged() (tadlib.hitad.aligner.DomainAligner method) minCore() (tadlib.hitad.chromLev.Chrom method) minWindows() (tadlib.hitad.chromLev.Chrom method) MultiReps (class in tadlib.hitad.chromLev)

N

NestedDomains() (tadlib.hitad.aligner.DomainSet method)

Node (class in tadlib.hitad.aligner)

O

oriHMMParams() (tadlib.hitad.genomeLev.Genome method) oriIter() (tadlib.hitad.chromLev.Chrom method)

oriWindow() (tadlib.hitad.chromLev.Chrom method) overlap() (tadlib.hitad.aligner.SingleDomain method)

P

pipe() (tadlib.hitad.chromLev.Chrom method)

plot() (tadlib.hitad.chromLev.Chrom method) Polygon (class in tadlib.calfea.polygon)

R

randomCheck() (tadlib.hitad.chromLev.Chrom method) readHierDomain() (in module tadlib.hitad.aligner)

readPlainDomain() (in module tadlib.hitad.aligner) refNoise() (tadlib.hitad.chromLev.Chrom method) reproducible() (tadlib.hitad.chromLev.MultiReps method)

S

scoreCache() (tadlib.hitad.chromLev.Chrom method) shoelace() (in module tadlib.calfea.polygon) SingleBound (class in tadlib.hitad.aligner) SingleDomain (class in tadlib.hitad.aligner)

split() (tadlib.hitad.aligner.DomainAligner method) splitChrom() (tadlib.hitad.chromLev.Chrom method) stablescore() (tadlib.hitad.chromLev.Chrom method) sub2tad() (tadlib.hitad.aligner.BoundAligner method) subDomains() (tadlib.hitad.chromLev.Chrom method)

T

tad2sub() (tadlib.hitad.aligner.BoundAligner method)

toArrowhead() (tadlib.hitad.chromLev.Chrom method) totalCover() (tadlib.calfea.analyze.Core method)

V

viterbi() (tadlib.hitad.chromLev.Chrom method)

W

wipeDisk() (tadlib.hitad.genomeLev.Genome method)