Ecosyste.ms: Issues

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GitHub / GangCaoLab/CoolBox issues and pull requests

#99 - 您好，可以画整个基因组互作吗？

Issue - State: open - Opened by Zheng19w 2 months ago

#98 - fix bug in issue #97

Pull Request - State: closed - Opened by wbszhu 2 months ago

#97 - TypeError in Arcs() due to Argument Mismatch with matplotlib.patches.Arc

Issue - State: closed - Opened by skelviper 3 months ago - 3 comments

#96 - Plot saving in API mode

Issue - State: open - Opened by DexinYang1998 3 months ago - 1 comment

#95 - Some error when plot GTF

Issue - State: closed - Opened by szbssg 5 months ago - 4 comments

#94 - Genomic position track

Issue - State: closed - Opened by MyBiscuit 6 months ago - 1 comment

#93 - Heatmap for tracks

Issue - State: closed - Opened by StarkTS98 6 months ago - 1 comment

#92 - Fixes issue https://github.com/GangCaoLab/CoolBox/issues/90

Pull Request - State: closed - Opened by ggilestro 7 months ago

#91 - Equal aspect for hic matrix

Pull Request - State: open - Opened by Phlya 7 months ago - 3 comments

#90 - Bug in GTF handling [patch offered]

Issue - State: closed - Opened by ggilestro 7 months ago - 1 comment

#88 - Strange behavior of bigwig visualization

Issue - State: open - Opened by camelest 9 months ago - 1 comment

#87 - plot entire genome

Issue - State: open - Opened by MyBiscuit 12 months ago

#86 - cool

Issue - State: closed - Opened by Zheng19w about 1 year ago - 1 comment

#85 - plot DNA feature error

Issue - State: open - Opened by yangfeizZZ about 1 year ago

#84 - Requesting Assistance with CoolBox Visualization - Achieving A/B compartments

Issue - State: open - Opened by wbszhu about 1 year ago - 2 comments

#83 - use with custom matplotlib figures

Issue - State: closed - Opened by Phlya about 1 year ago - 2 comments

#82 - TAD Image generation error

Issue - State: closed - Opened by Zheng19w about 1 year ago - 3 comments

#81 - No insulation score is being plotted

Issue - State: closed - Opened by MyBiscuit about 1 year ago

#80 - Cool.fetch_data problem

Issue - State: closed - Opened by MyBiscuit about 1 year ago - 2 comments

#79 - joint view two different cool files

Issue - State: open - Opened by EnrichettaMileti over 1 year ago - 1 comment

#78 - How do I save a figure to a file?

Issue - State: closed - Opened by ianakim over 1 year ago

#77 - Installation fail with pip python3.9

Issue - State: open - Opened by xunchen85 over 1 year ago - 4 comments

#76 - Increase fontsize of GTF

Issue - State: open - Opened by gdolsten over 1 year ago

#75 - Change aspect ratio of jointview

Issue - State: open - Opened by gdolsten over 1 year ago

#73 - Missing arcs when plotting BEDPE file format

Issue - State: open - Opened by eafyounian almost 2 years ago - 1 comment
Labels: bug

#72 - Apply CoolBox to the transcript coordinate system

Issue - State: open - Opened by ifantasy about 2 years ago
Labels: enhancement

#71 - How to use parameters from Class in the CLI mode?

Issue - State: closed - Opened by shunliubio about 2 years ago - 1 comment

#70 - A few bugs in loops (arcs) and Hi-C Heatmap body.

Issue - State: open - Opened by Linhua-Sun over 2 years ago - 1 comment
Labels: bug

#69 - Is it possibile to add highlight regions on Hi-C heatmap body horizontally?

Issue - State: open - Opened by Linhua-Sun over 2 years ago - 3 comments
Labels: enhancement

#68 - Docker installation correction

Issue - State: open - Opened by skr3178 over 2 years ago

#67 - [feature request]collinear view

Issue - State: open - Opened by jksr over 2 years ago - 2 comments
Labels: enhancement

#66 - bug when plotting gtf?

Issue - State: open - Opened by jksr over 2 years ago - 1 comment
Labels: bug

#65 - Couldn't change bin width of histgram

Issue - State: closed - Opened by zhouzhendiao over 2 years ago - 7 comments

#63 - is there a way to annotate with text

Issue - State: closed - Opened by jksr over 2 years ago - 1 comment

#62 - Squish bed file visualization

Issue - State: closed - Opened by perinom over 2 years ago - 2 comments

#61 - Problem with displaying Ideograms

Issue - State: closed - Opened by nneretti over 2 years ago - 2 comments

#60 - error in doctool: `param` does not have a `name` attribute

Issue - State: closed - Opened by rekado over 2 years ago - 3 comments

#59 - Jointview doesn't work with HiCPeaksCoverage

Issue - State: open - Opened by gdolsten over 2 years ago
Labels: bug

#58 - Coolbox and GTF

Issue - State: closed - Opened by gdolsten over 2 years ago - 3 comments

#57 - Frame.plot closes figure

Issue - State: closed - Opened by scyrusm almost 3 years ago - 1 comment

#56 - JointView fails for .hic files

Issue - State: closed - Opened by tuomovirtanen almost 3 years ago - 1 comment

#55 - How is insulation score calculation performed?

Issue - State: closed - Opened by gdolsten almost 3 years ago - 3 comments

#54 - Is it possible to have multiple looping arcs in one track?

Issue - State: closed - Opened by gdolsten almost 3 years ago - 2 comments

#53 - bed9 detected as a bed6

Issue - State: open - Opened by alexlenail almost 3 years ago - 2 comments

#52 - Support more of pyGenomeTracks' parameters

Issue - State: open - Opened by alexlenail almost 3 years ago
Labels: enhancement

#51 - AttributeError: 'YAxis' object has no attribute '_gridOnMajor'

Issue - State: closed - Opened by alexlenail almost 3 years ago - 2 comments

#50 - Allowing XAxis() to show lengths in bp in addition to kb

Issue - State: closed - Opened by c-guzman almost 3 years ago - 2 comments

#49 - Changing the way a track looks

Issue - State: closed - Opened by c-guzman almost 3 years ago - 8 comments
Labels: help wanted

#48 - Error when trying to parse a custom fasta/bedgraph

Issue - State: open - Opened by c-guzman almost 3 years ago - 3 comments
Labels: bug

#47 - Heatmap of hi-c became asymmetric in size

Issue - State: open - Opened by Linhua-Sun about 3 years ago
Labels: bug

#46 - Citing CoolBox

Issue - State: closed - Opened by eafyounian about 3 years ago - 4 comments

#45 - The coordinates of loops are misplaced

Issue - State: closed - Opened by Linhua-Sun about 3 years ago - 5 comments
Labels: bug

#44 - Can coolbox create non-symmetric heatmaps?

Issue - State: open - Opened by Linhua-Sun about 3 years ago - 5 comments
Labels: enhancement

#43 - CoolBox doesn't work with for loops?

Issue - State: closed - Opened by gdolsten about 3 years ago - 2 comments

#42 - Is there a way to visualize qualitative data?

Issue - State: closed - Opened by gdolsten about 3 years ago - 6 comments
Labels: enhancement

#41 - add libcurl dep

Pull Request - State: closed - Opened by Nanguage about 3 years ago

#40 - failed with juicer's .hic format files

Issue - State: closed - Opened by Linhua-Sun about 3 years ago - 8 comments
Labels: bug

#39 - Possibility to change positional argument in `coolbox.core.track.HiCMat()` to named argument

Issue - State: closed - Opened by eafyounian about 3 years ago - 2 comments
Labels: good first issue

#38 - Changing resolution for hic matrix is not working

Issue - State: closed - Opened by tuomovirtanen about 3 years ago - 2 comments
Labels: bug, help wanted

#37 - UnicodeDecodeError in Browser with parameter img_format different than svg.

Issue - State: closed - Opened by eafyounian about 3 years ago - 4 comments

#36 - auto build doc

Issue - State: open - Opened by zhqu1148980644 about 3 years ago - 1 comment
Labels: enhancement

#35 - improve documentation readability

Pull Request - State: closed - Opened by eafyounian about 3 years ago - 8 comments

#34 - Update installation.md

Pull Request - State: closed - Opened by eafyounian about 3 years ago - 1 comment

#33 - hieght of BED track is too large

Issue - State: closed - Opened by zhqu1148980644 about 3 years ago - 1 comment
Labels: enhancement

#32 - Empty gtf plot caused by row_filter in GTF track

Issue - State: open - Opened by zhqu1148980644 about 3 years ago
Labels: enhancement

#31 - Staircase plot style for Hist

Pull Request - State: closed - Opened by nvictus about 3 years ago - 1 comment

#30 - refactor code by sourcery

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago

#29 - Reset file_handle to avoid skipping the first interval for visualization

Pull Request - State: closed - Opened by wkopp over 3 years ago - 2 comments

#28 - docker: invalid reference format: repository name must be lowercase.

Issue - State: closed - Opened by mdozmorov over 3 years ago - 3 comments

#27 - Ignore convertion to float for some properties

Pull Request - State: closed - Opened by wkopp over 3 years ago - 1 comment

#26 - bed_type needed to be set earlier

Pull Request - State: closed - Opened by wkopp over 3 years ago

#25 - fix bug in joint_view mode by swap genomerange

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago

#24 - merge to master

Pull Request - State: closed - Opened by Nanguage over 3 years ago

#23 - Doc inheritance

Issue - State: closed - Opened by Nanguage over 3 years ago - 2 comments

#22 - restore requiremnts.txt

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago

#21 - Reuse plot codes of arcs, hicpeaks

Issue - State: closed - Opened by zhqu1148980644 over 3 years ago - 2 comments

#20 - undesired bed plot

Issue - State: closed - Opened by zhqu1148980644 over 3 years ago - 2 comments
Labels: bug

#19 - Allow jointview with no side tracks

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago - 6 comments

#18 - Add cli support for joint_view

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago

#17 - Add Peakachu track as example in doc

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago

#16 - add fetch_data and gallery for JointView

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago - 1 comment

#15 - Expand fetching region in IS and DI track to fill the border gap.

Issue - State: open - Opened by Nanguage over 3 years ago
Labels: enhancement

#14 - Add window_size ranges for InsuScore, Heatmap support for Hist

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago - 1 comment

#13 - Multiple window size IS score visulization

Issue - State: closed - Opened by Nanguage over 3 years ago

#12 - JointView proposal

Issue - State: closed - Opened by Nanguage over 3 years ago

#11 - Refractor hist.hicfeature module

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago - 1 comment

#10 - HiCFeature should support input a path to a .hic/.cool file

Issue - State: closed - Opened by Nanguage over 3 years ago - 1 comment

#9 - Add document to TAD and IS track

Issue - State: closed - Opened by Nanguage over 3 years ago - 1 comment

#8 - Add insu_score and di_score track

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago

#7 - Update python-package-conda.yml

Pull Request - State: closed - Opened by zhqu1148980644 over 3 years ago

#6 - feature request: plot on given axes

Issue - State: closed - Opened by jksr over 4 years ago - 1 comment

#5 - How to overlay bigwigs?

Issue - State: closed - Opened by Benfeitas over 4 years ago - 1 comment

#4 - Can't plot Frame with HicCompare

Issue - State: closed - Opened by azkalot1 almost 5 years ago - 1 comment

#3 - Feature request: multiprocessing

Issue - State: open - Opened by iamjli almost 5 years ago - 1 comment
Labels: enhancement

#2 - Feature request: colored arcs

Issue - State: closed - Opened by iamjli almost 5 years ago - 6 comments

#1 - Feature request

Issue - State: open - Opened by gegenhu about 5 years ago - 1 comment
Labels: enhancement