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
#151 - No chromosomes are in common between the coordinate file and the cooler file.
Issue -
State: closed - Opened by ratheraarif 3 months ago
- 9 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
#146 - `pu.pileupsWithControl` might skip some pile-up regions or raise vague `domain_score not in dict2` AssertionError
Issue -
State: open - Opened by nvaulin 4 months ago
- 1 comment
#145 - [Q] Setting --mindist parameter as 0, but not contain all number of loop(input loop.bedpe)
Issue -
State: open - Opened by Datacond 5 months ago
- 3 comments
#144 - To access a value by position, use `ser.iloc[pos]` chroffset = self.clr.offset(region[0])
Issue -
State: open - Opened by jiangshan529 6 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
#139 - [Q] Question on normalization between 2 conditions before coolpups
Issue -
State: open - Opened by Lucas446 10 months ago
#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
#135 - ValueError: operands could not be broadcast together with shapes (125,125) (127,127)
Issue -
State: closed - Opened by NMaziak 12 months ago
- 4 comments
#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
#132 - [Q]Why is Pile-ups of interactions between a set of regions is so time cosuming?
Issue -
State: closed - Opened by jiangshan529 over 1 year ago
- 21 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
#126 - Argument `expected_value_col` in PileUpper methods is ignored
Issue -
State: closed - Opened by hisakatha over 1 year ago
#125 - cooltools pileup for CTCF and RAD21
Issue -
State: closed - Opened by odovgusha over 1 year ago
- 6 comments
#124 - [Q]When the new version performs rescaling pileup analysis, there is a problem with the ignore_diags parameter
Issue -
State: closed - Opened by WANGchuang715 over 1 year ago
- 5 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
#117 - [Q] How to calculate the significance of clustering difference between to comparison groups?
Issue -
State: closed - Opened by YuboWang1994 almost 2 years ago
- 2 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
#107 - Resolution compatibility between .cool file and .bedpe file for pile-ups of predefined regions pairs
Issue -
State: closed - Opened by Soh-hyon almost 2 years ago
- 1 comment
#106 - saddle plot score
Issue -
State: closed - Opened by BenxiaHu almost 2 years ago
- 1 comment
#105 - Added groupby option to CLI. Version number saved in metadata. Removed incl_chrs and excl_chrs
Pull Request -
State: closed - Opened by efriman 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
#92 - Col/row sorting as in --input_pups are sorted in input unless otherwise specified
Pull Request -
State: closed - Opened by efriman about 2 years ago
#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
#86 - Recreating figure: And here is a real example of CTCF-associated loops in ES cells:
Issue -
State: closed - Opened by mattbramble about 2 years ago
- 5 comments
#85 - Study the correlation scaled pile up (aggregated) plot of TADs with box plot of TADs strength
Issue -
State: closed - Opened by sachingadakh about 2 years ago
- 15 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
#81 - Changed flip_negative strand behaviour to work properly for non-local pileups
Pull Request -
State: closed - Opened by efriman about 2 years ago
#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