Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / open2c/coolpuppy issues and pull requests

#156 - A large number of NAs ​​appear on the diagonal[Q]

Issue - State: closed - Opened by G1298192734a 3 months ago - 1 comment

#155 - TypeError: unsupported operand type(s) for +: 'int' and 'str'

Issue - State: open - Opened by ratheraarif 3 months ago - 4 comments

#154 - Notebook test fixes

Pull Request - State: closed - Opened by efriman 3 months ago - 1 comment

#153 - [BUG]Labels messed up in plot_stripes lineplot=Treu

Issue - State: closed - Opened by zhaoyycrow 3 months ago - 2 comments

#152 - [Q]Understanding rescaling

Issue - State: closed - Opened by zhaoyycrow 3 months ago - 2 comments

#150 - Pileup for telomeres concerning trans chromosomal interactions

Issue - State: closed - Opened by Brahmandam-Gayatri 4 months ago - 26 comments

#149 - [Q]loop analysis takes long time

Issue - State: closed - Opened by jiangshan529 4 months ago - 6 comments

#148 - [Q] How to test significance of change between pileups?

Issue - State: open - Opened by AudreyBaguette 4 months ago - 1 comment

#147 - [BUG]Import error `from coolpuppy import plotpup`

Issue - State: closed - Opened by zhaoyycrow 4 months ago - 2 comments

#143 - Extracting locus strength scores for loops

Issue - State: open - Opened by NMaziak 6 months ago - 3 comments

#142 - Y-Axis labels missing with plotpup.plot

Issue - State: closed - Opened by linus3210 6 months ago - 1 comment

#141 - [Q]How to get the matrix data after running coolpup.py

Issue - State: closed - Opened by valderpan 7 months ago - 3 comments

#140 - dividepups.py error

Issue - State: closed - Opened by BenxiaHu 9 months ago - 2 comments

#138 - Can coolpuppy use raw cool file to perform analysis?

Issue - State: closed - Opened by JiaoLaboratory 10 months ago - 4 comments

#137 - how to generate a my_hic_data_expected.tsv ?

Issue - State: closed - Opened by JiaoLaboratory 11 months ago

#136 - how to generate the expected.tsv?[Q]

Issue - State: closed - Opened by JiaoLaboratory 11 months ago - 1 comment

#134 - [Q]ValueError: Too few columns

Issue - State: closed - Opened by jiangshan529 about 1 year ago - 2 comments

#133 - About plotpup.py error

Issue - State: closed - Opened by GleeenSIBS over 1 year ago - 5 comments

#131 - Load/reoder chromosomes

Issue - State: closed - Opened by odovgusha over 1 year ago - 1 comment

#130 - Added ignore_group_order argument

Pull Request - State: closed - Opened by efriman over 1 year ago - 7 comments

#129 - providing an array as argument for by_distance

Issue - State: closed - Opened by hadirah87 over 1 year ago - 2 comments

#128 - APA score

Issue - State: closed - Opened by BenxiaHu over 1 year ago - 19 comments

#127 - Fix #126 where an argument (expected_value_col) for normalization in pileup is ignored

Pull Request - State: closed - Opened by hisakatha over 1 year ago - 2 comments

#125 - cooltools pileup for CTCF and RAD21

Issue - State: closed - Opened by odovgusha over 1 year ago - 6 comments

#123 - [Q]Error in Apa

Issue - State: closed - Opened by ag-abhishek over 1 year ago - 2 comments

#122 - [Q]question about normalization

Issue - State: closed - Opened by jiangshan529 over 1 year ago - 3 comments

#121 - [Q]why is the middle value not in the center of the color bar

Issue - State: closed - Opened by jiangshan529 over 1 year ago - 9 comments

#120 - [Q]only two huge squares in the final plot

Issue - State: closed - Opened by jiangshan529 over 1 year ago - 3 comments

#119 - [Q]why the value on heatmap is zero

Issue - State: closed - Opened by jiangshan529 almost 2 years ago - 9 comments

#118 - [Q]installing problem

Issue - State: closed - Opened by jiangshan529 almost 2 years ago - 7 comments

#116 - lineplot and divide_pups small fixes

Pull Request - State: closed - Opened by efriman almost 2 years ago

#115 - How does rescale work?

Issue - State: closed - Opened by Jason-Qiuhai almost 2 years ago - 2 comments

#114 - Added debug for peak duplicates. Small fixes lineplot

Pull Request - State: closed - Opened by efriman almost 2 years ago - 1 comment

#113 - how to plot interchromosome interactions

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

#112 - Added dtypes and column number checks for CLI features

Pull Request - State: closed - Opened by efriman almost 2 years ago

#111 - how to plot short and long contact frequency

Issue - State: closed - Opened by BenxiaHu almost 2 years ago - 6 comments

#110 - No chromosomes are in common

Issue - State: closed - Opened by Jason-Qiuhai almost 2 years ago - 9 comments

#109 - coverage_norm fix for new cooltools coverage. Fixed multiprocessing for python>=3.9.13

Pull Request - State: closed - Opened by efriman almost 2 years ago - 1 comment

#108 - Add "lib" submodule

Pull Request - State: closed - Opened by dongbohu almost 2 years ago - 1 comment

#106 - saddle plot score

Issue - State: closed - Opened by BenxiaHu almost 2 years ago - 1 comment

#104 - Install error: module 'coolpuppy.lib'

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

#103 - Moved plotpup.py into coolpuppy folder. Plot logging. Minor plotting tweaks

Pull Request - State: closed - Opened by efriman about 2 years ago - 1 comment

#102 - how to plot difference

Issue - State: closed - Opened by BenxiaHu about 2 years ago - 6 comments

#101 - saddle plot

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

#100 - heatmap value

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

#99 - coverage_norm incompatible with unreleased cooltools

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

#98 - plot TAD error

Issue - State: closed - Opened by BenxiaHu about 2 years ago - 6 comments

#97 - installation error

Issue - State: closed - Opened by BenxiaHu about 2 years ago - 12 comments

#96 - Minor plotting tweaks

Pull Request - State: closed - Opened by efriman about 2 years ago - 2 comments

#95 - User facing convenient functions

Pull Request - State: closed - Opened by Phlya about 2 years ago - 1 comment

#94 - Restructure

Pull Request - State: closed - Opened by Phlya about 2 years ago - 1 comment

#93 - Bug fixes

Pull Request - State: closed - Opened by efriman about 2 years ago - 1 comment

#91 - Major plotting tweaks

Pull Request - State: closed - Opened by efriman about 2 years ago - 1 comment

#90 - [plotpup.py] How to draw multiple plots at once?

Issue - State: closed - Opened by Soh-hyon about 2 years ago - 10 comments

#89 - How to deal with KeyError and ValueError?

Issue - State: closed - Opened by Soh-hyon about 2 years ago - 2 comments

#88 - Store scores

Pull Request - State: closed - Opened by Phlya about 2 years ago - 1 comment

#87 - ImportError: cannot import name 'snipping' from 'cooltools'

Issue - State: closed - Opened by Irenexzwen about 2 years ago - 4 comments

#84 - Hdf5 optimized saving for stripes, compression options

Pull Request - State: closed - Opened by efriman about 2 years ago - 1 comment

#83 - Add coverage using cooltools.coverage

Pull Request - State: closed - Opened by Phlya about 2 years ago

#82 - confused on parameter

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

#80 - Divide pileups, plotting tweaks

Pull Request - State: closed - Opened by efriman about 2 years ago - 1 comment

#79 - I got different results from the example with test data

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

#78 - Add feature to divide two pileups and plot

Issue - State: closed - Opened by efriman about 2 years ago

#77 - Fixed bug where NaNs were incorrectly marked

Pull Request - State: closed - Opened by efriman about 2 years ago

#76 - Fixed tutorial png

Pull Request - State: closed - Opened by efriman over 2 years ago - 1 comment

#75 - Updated tutorials. Minor fixes

Pull Request - State: closed - Opened by efriman over 2 years ago - 1 comment

#74 - Hdf5-saving stripes

Pull Request - State: closed - Opened by efriman over 2 years ago

#73 - plotpup.py TypeError: __init__() got an unexpected keyword argument 'add_all'

Issue - State: open - Opened by odovgusha over 2 years ago - 2 comments

#72 - ValueError: invalid literal for int() with base 10: '.\n'

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

#71 - Bug fixes, font selection, by_distance edge selection using CLI

Pull Request - State: closed - Opened by efriman over 2 years ago - 1 comment

#70 - API saving add 'features'

Issue - State: closed - Opened by efriman over 2 years ago

#69 - Fix coverage for trans

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

#68 - KeyError: 'coordinates'

Issue - State: closed - Opened by iagooteroc over 2 years ago - 10 comments

#67 - coolpup.py Pile-ups of predefined regions pairs,

Issue - State: closed - Opened by mb6434 over 2 years ago - 4 comments

#66 - Fixed inverted second half of corner stripe

Pull Request - State: closed - Opened by efriman over 2 years ago

#65 - Fixed corner_stripe inversion bug

Pull Request - State: closed - Opened by efriman over 2 years ago

#64 - Merge from trans branch

Pull Request - State: closed - Opened by efriman over 2 years ago - 1 comment

#63 - Merge with trans, bug fixes

Pull Request - State: closed - Opened by efriman over 2 years ago - 1 comment

#62 - Merge with trans

Pull Request - State: closed - Opened by efriman over 2 years ago - 1 comment

#61 - Fixed bugs with rescaling. renamed fraction_flank to rescale_flank

Pull Request - State: closed - Opened by efriman over 2 years ago

#60 - Merge

Pull Request - State: closed - Opened by efriman over 2 years ago

#59 - coolpup.py snipping from cooltools error

Issue - State: closed - Opened by yloemie over 2 years ago - 5 comments

#58 - Update tutorials

Issue - State: closed - Opened by efriman over 2 years ago

#57 - Stripe saving inefficient, hdf5-optimize

Issue - State: closed - Opened by efriman over 2 years ago