Index

A

abspath() (in module coolbox.utilities) add() (coolbox.utilities.IntervalTree method) addi() (coolbox.utilities.IntervalTree method) append() (coolbox.utilities.deque method) (coolbox.utilities.IntervalTree method) append_coverage() (coolbox.core.track.Track method) appendi() (coolbox.utilities.IntervalTree method)

appendleft() (coolbox.utilities.deque method) Arcs() (in module coolbox.core.coverage) (in module coolbox.core.track) ArcsBase (class in coolbox.core.track) ArcsCoverage (class in coolbox.core.coverage) args (coolbox.utilities.partial attribute) at() (coolbox.utilities.IntervalTree method)

B

BAM (class in coolbox.core.track) BAMCov (class in coolbox.core.track) BED (class in coolbox.core.track) BedBase (class in coolbox.core.track) BedGraph (class in coolbox.core.coverage) (class in coolbox.core.track) BedGraphCoverage (class in coolbox.core.coverage) BEDPE (class in coolbox.core.coverage) (class in coolbox.core.track)

BEDPECoverage (class in coolbox.core.coverage) begin() (coolbox.utilities.IntervalTree method) BigWig (class in coolbox.core.coverage) (class in coolbox.core.track) BigWigCoverage (class in coolbox.core.coverage) bound_range() (coolbox.utilities.GenomeLength method) Browser (class in coolbox.core.browser)

C

change_chrom_names() (coolbox.utilities.GenomeRange method) (in module coolbox.utilities) check_range() (coolbox.utilities.GenomeLength method) chop() (coolbox.utilities.IntervalTree method) ChromName (class in coolbox.core.track) clear() (coolbox.utilities.deque method) (coolbox.utilities.IntervalTree method) clear_fig_cache() (coolbox.core.browser.Browser method) cm2inch() (in module coolbox.utilities) Color (class in coolbox.core.feature) ColorMap (class in coolbox.core.feature) contains_interval() (coolbox.utilities.Interval method) contains_point() (coolbox.utilities.Interval method) containsi() (coolbox.utilities.IntervalTree method) Cool (class in coolbox.core.track) coolbox.core.browser module

coolbox.core.coverage module coolbox.core.feature module coolbox.core.frame module coolbox.core.track module coolbox.utilities module CoolStyle (class in coolbox.core.feature) copy() (coolbox.utilities.deque method) (coolbox.utilities.Interval method) (coolbox.utilities.IntervalTree method) correspond_track() (in module coolbox.utilities) count() (coolbox.utilities.deque method)

D

DepthRatio (class in coolbox.core.feature) deque (class in coolbox.utilities) difference() (coolbox.utilities.IntervalTree method) difference_update() (coolbox.utilities.IntervalTree method) dirname() (in module coolbox.utilities)

discard() (coolbox.utilities.IntervalTree method) discardi() (coolbox.utilities.IntervalTree method) DiScore (class in coolbox.core.track) distance_to() (coolbox.utilities.Interval method) DotHiC (class in coolbox.core.track)

E

end() (coolbox.utilities.IntervalTree method) envelop() (coolbox.utilities.IntervalTree method)

extend() (coolbox.utilities.deque method) extendleft() (coolbox.utilities.deque method)

F

Feature (class in coolbox.core.feature) fetch_data() (coolbox.core.coverage.BedGraph method) (coolbox.core.coverage.BEDPE method) (coolbox.core.coverage.BigWig method) (coolbox.core.coverage.Pairs method) (coolbox.core.track.BAM method) (coolbox.core.track.BAMCov method) (coolbox.core.track.BedBase method) (coolbox.core.track.BedGraph method) (coolbox.core.track.BEDPE method) (coolbox.core.track.BigWig method) (coolbox.core.track.ChromName method) (coolbox.core.track.Cool method) (coolbox.core.track.DiScore method) (coolbox.core.track.DotHiC method) (coolbox.core.track.GTF method) (coolbox.core.track.HiCDiff method) (coolbox.core.track.HicMatBase method) (coolbox.core.track.HistBase method) (coolbox.core.track.HLine method) (coolbox.core.track.Ideogram method) (coolbox.core.track.InsuScore method) (coolbox.core.track.Pairs method) (coolbox.core.track.Selfish method) (coolbox.core.track.SNP method) (coolbox.core.track.Spacer method) (coolbox.core.track.Track method) (coolbox.core.track.Virtual4C method) (coolbox.core.track.XAxis method)

fetch_intervals() (coolbox.core.track.GTF method) fetch_pixels() (coolbox.core.track.Cool method) (coolbox.core.track.DotHiC method) fetch_plot_data() (coolbox.core.coverage.BedGraph method) (coolbox.core.coverage.BEDPE method) (coolbox.core.coverage.BigWig method) (coolbox.core.track.ArcsBase method) (coolbox.core.track.BedGraph method) (coolbox.core.track.BEDPE method) (coolbox.core.track.BigWig method) (coolbox.core.track.HicMatBase method) (coolbox.core.track.HistBase method) (coolbox.core.track.SNP method) (coolbox.core.track.Track method) fetch_scores() (coolbox.core.coverage.BigWig method) (coolbox.core.track.BigWig method) fig2bytes() (in module coolbox.utilities) file_to_intervaltree() (in module coolbox.utilities) find_nested() (coolbox.utilities.IntervalTree method) format_properties() (in module coolbox.utilities) FrameFeature (class in coolbox.core.feature) FrameTitle (class in coolbox.core.feature) from_tuples() (coolbox.utilities.IntervalTree class method) func (coolbox.utilities.partial attribute)

G

ge() (coolbox.utilities.Interval method) GenomeLength (class in coolbox.utilities) GenomeRange (class in coolbox.utilities) get_bed_interval() (coolbox.utilities.ReadBed method) get_init_range() (coolbox.core.browser.Browser method) get_no_comment_line() (coolbox.utilities.ReadBed method)

get_size() (in module coolbox.utilities) get_tmp_dir() (in module coolbox.utilities) get_uniq_tmp_file() (in module coolbox.utilities) gt() (coolbox.utilities.Interval method) GTF (class in coolbox.core.track) guess_file_type() (coolbox.utilities.ReadBed method)

H

hex2rgb() (in module coolbox.utilities) HiCDiff (class in coolbox.core.track) HiCMat() (in module coolbox.core.track) HicMatBase (class in coolbox.core.track) HiCPeaks (class in coolbox.core.coverage) (class in coolbox.core.track) HiCPeaksCoverage (class in coolbox.core.coverage) HighLights (class in coolbox.core.coverage)

HighLightsFromFile (class in coolbox.core.coverage) Hist() (in module coolbox.core.coverage) (in module coolbox.core.track) HistBase (class in coolbox.core.track) HistCoverage (class in coolbox.core.coverage) HistStyle (class in coolbox.core.feature) HLine (class in coolbox.core.track) HLines (class in coolbox.core.coverage)

I

Ideogram (class in coolbox.core.track) inch2cm() (in module coolbox.utilities) index() (coolbox.utilities.deque method) insert() (coolbox.utilities.deque method) InsuScore (class in coolbox.core.track) intersection() (coolbox.utilities.IntervalTree method) intersection_update() (coolbox.utilities.IntervalTree method)

Interval (class in coolbox.utilities) IntervalTree (class in coolbox.utilities) Inverted (class in coolbox.core.feature) is_empty() (coolbox.utilities.IntervalTree method) is_null() (coolbox.utilities.Interval method) items() (coolbox.utilities.IntervalTree method) iter() (coolbox.utilities.IntervalTree method)

J

join() (in module coolbox.utilities)

K

keywords (coolbox.utilities.partial attribute)

L

le() (coolbox.utilities.Interval method) length (coolbox.utilities.GenomeRange property)

length() (coolbox.utilities.Interval method) lt() (coolbox.utilities.Interval method)

M

maxlen (coolbox.utilities.deque attribute) MaxValue (class in coolbox.core.feature) merge_equals() (coolbox.utilities.IntervalTree method) merge_overlaps() (coolbox.utilities.IntervalTree method) MinValue (class in coolbox.core.feature) module coolbox.core.browser coolbox.core.coverage coolbox.core.feature coolbox.core.frame coolbox.core.track coolbox.utilities

N

next() (coolbox.utilities.ReadBed method)

O

op_err_msg() (in module coolbox.utilities) opener() (in module coolbox.utilities) overlap() (coolbox.utilities.IntervalTree method) overlap_size() (coolbox.utilities.Interval method)

overlaps() (coolbox.utilities.Interval method) (coolbox.utilities.IntervalTree method) overlaps_point() (coolbox.utilities.IntervalTree method) overlaps_range() (coolbox.utilities.IntervalTree method)

P

Pairs (class in coolbox.core.coverage) (class in coolbox.core.track) PairsCoverage (class in coolbox.core.coverage) parse_region_string() (coolbox.utilities.GenomeRange static method) partial (class in coolbox.utilities) pile_coverages() (coolbox.core.track.Track method) plot() (coolbox.core.coverage.TAD method) (coolbox.core.track.ArcsBase method) (coolbox.core.track.BAM method) (coolbox.core.track.BED method) (coolbox.core.track.ChromName method) (coolbox.core.track.GTF method) (coolbox.core.track.HicMatBase method) (coolbox.core.track.HistBase method) (coolbox.core.track.HLine method) (coolbox.core.track.Ideogram method) (coolbox.core.track.Spacer method) (coolbox.core.track.TAD method) (coolbox.core.track.Track method) (coolbox.core.track.XAxis method)

plot_coverages() (coolbox.core.track.Track method) pop() (coolbox.utilities.deque method) popleft() (coolbox.utilities.deque method) preload_imgs() (coolbox.core.browser.Browser method) print_structure() (coolbox.utilities.IntervalTree method)

Q

query_bed() (in module coolbox.utilities)

R

range() (coolbox.utilities.IntervalTree method) range_matches() (coolbox.utilities.Interval method) ReadBed (class in coolbox.utilities) refGeneRec (class in coolbox.utilities) refresh() (coolbox.core.browser.Browser method) remove() (coolbox.utilities.deque method) (coolbox.utilities.IntervalTree method)

remove_envelop() (coolbox.utilities.IntervalTree method) remove_overlap() (coolbox.utilities.IntervalTree method) removei() (coolbox.utilities.IntervalTree method) reverse() (coolbox.utilities.deque method) rgb2hex() (in module coolbox.utilities) rotate() (coolbox.utilities.deque method)

S

save() (coolbox.core.browser.Browser method) score() (coolbox.utilities.IntervalTree method) Selfish (class in coolbox.core.track) set_colormap() (coolbox.core.track.BedBase method) shiftedColorMap() (in module coolbox.utilities) show() (coolbox.core.browser.Browser method) ShowColorBar (class in coolbox.core.feature) ShowDataRange (class in coolbox.core.feature)

slice() (coolbox.utilities.IntervalTree method) SNP (class in coolbox.core.track) Spacer (class in coolbox.core.track) span() (coolbox.utilities.IntervalTree method) split_genome_range() (in module coolbox.utilities) split_overlaps() (coolbox.utilities.IntervalTree method) symmetric_difference() (coolbox.utilities.IntervalTree method) symmetric_difference_update() (coolbox.utilities.IntervalTree method)

T

tabix_index() (in module coolbox.utilities) tabix_query() (in module coolbox.utilities) TAD (class in coolbox.core.coverage) (class in coolbox.core.track) TADCoverage (class in coolbox.core.coverage)

Title (class in coolbox.core.feature) to_bytes() (in module coolbox.utilities) to_gr() (in module coolbox.utilities) to_string() (in module coolbox.utilities) Track (class in coolbox.core.track) TrackHeight (class in coolbox.core.feature)

U

union() (coolbox.utilities.IntervalTree method)

update() (coolbox.utilities.IntervalTree method)

V

verify() (coolbox.utilities.IntervalTree method) Virtual4C (class in coolbox.core.track)

Vlines (class in coolbox.core.coverage) VlinesFromFile (class in coolbox.core.coverage)

W

WidgetsPanel (class in coolbox.core.browser)

X

XAxis (class in coolbox.core.track)