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open2c
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coolpuppy
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
MIT License
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A large number of NAs appear on the diagonal[Q]
#156
G1298192734a
closed
1 week ago
1
TypeError: unsupported operand type(s) for +: 'int' and 'str'
#155
ratheraarif
opened
2 weeks ago
4
Notebook test fixes
#154
efriman
closed
1 week ago
1
[BUG]Labels messed up in plot_stripes lineplot=Treu
#153
zhaoyycrow
closed
6 hours ago
2
[Q]Understanding rescaling
#152
zhaoyycrow
opened
4 weeks ago
1
No chromosomes are in common between the coordinate file and the cooler file.
#151
ratheraarif
closed
4 weeks ago
9
Pileup for telomeres concerning trans chromosomal interactions
#150
Brahmandam-Gayatri
closed
1 month ago
26
[Q]loop analysis takes long time
#149
jiangshan529
closed
1 month ago
6
[Q] How to test significance of change between pileups?
#148
AudreyBaguette
opened
1 month ago
1
[BUG]Import error `from coolpuppy import plotpup`
#147
zhaoyycrow
closed
1 month ago
2
`pu.pileupsWithControl` might skip some pile-up regions or raise vague `domain_score not in dict2` AssertionError
#146
nvaulin
opened
2 months ago
1
[Q] Setting --mindist parameter as 0, but not contain all number of loop(input loop.bedpe)
#145
Miracle-Yao
opened
2 months ago
3
To access a value by position, use `ser.iloc[pos]` chroffset = self.clr.offset(region[0])
#144
jiangshan529
opened
3 months ago
2
Extracting locus strength scores for loops
#143
NMaziak
opened
4 months ago
3
Y-Axis labels missing with plotpup.plot
#142
linus3210
closed
4 months ago
1
[Q]How to get the matrix data after running coolpup.py
#141
valderpan
closed
5 months ago
3
dividepups.py error
#140
BenxiaHu
closed
6 months ago
2
[Q] Question on normalization between 2 conditions before coolpups
#139
Lucas446
opened
7 months ago
0
Can coolpuppy use raw cool file to perform analysis?
#138
JiaoLaboratory
closed
8 months ago
4
how to generate a my_hic_data_expected.tsv ?
#137
JiaoLaboratory
closed
8 months ago
0
how to generate the expected.tsv?[Q]
#136
JiaoLaboratory
closed
8 months ago
1
ValueError: operands could not be broadcast together with shapes (125,125) (127,127)
#135
NMaziak
closed
4 months ago
4
[Q]ValueError: Too few columns
#134
jiangshan529
closed
9 months ago
2
About plotpup.py error
#133
GleeenSIBS
closed
1 year ago
5
[Q]Why is Pile-ups of interactions between a set of regions is so time cosuming?
#132
jiangshan529
closed
1 year ago
21
Load/reoder chromosomes
#131
odovgusha
closed
1 year ago
1
Added ignore_group_order argument
#130
efriman
closed
1 year ago
7
providing an array as argument for by_distance
#129
hrahmanin
closed
1 year ago
2
APA score
#128
BenxiaHu
closed
1 year ago
19
Fix #126 where an argument (expected_value_col) for normalization in pileup is ignored
#127
hisakatha
closed
1 year ago
2
Argument `expected_value_col` in PileUpper methods is ignored
#126
hisakatha
closed
1 year ago
0
cooltools pileup for CTCF and RAD21
#125
odovgusha
closed
1 year ago
6
[Q]When the new version performs rescaling pileup analysis, there is a problem with the ignore_diags parameter
#124
WANGchuang715
closed
1 year ago
5
[Q]Error in Apa
#123
ag-abhishek
closed
1 year ago
2
[Q]question about normalization
#122
jiangshan529
closed
1 year ago
3
[Q]why is the middle value not in the center of the color bar
#121
jiangshan529
closed
1 year ago
9
[Q]only two huge squares in the final plot
#120
jiangshan529
closed
1 year ago
3
[Q]why the value on heatmap is zero
#119
jiangshan529
closed
1 year ago
9
[Q]installing problem
#118
jiangshan529
closed
1 year ago
7
[Q] How to calculate the significance of clustering difference between to comparison groups?
#117
YuboWang1994
closed
1 year ago
2
lineplot and divide_pups small fixes
#116
efriman
closed
1 year ago
0
How does rescale work?
#115
Jason-Qiuhai
closed
1 year ago
2
Added debug for peak duplicates. Small fixes lineplot
#114
efriman
closed
1 year ago
1
how to plot interchromosome interactions
#113
BenxiaHu
closed
1 year ago
2
Added dtypes and column number checks for CLI features
#112
efriman
closed
1 year ago
0
how to plot short and long contact frequency
#111
BenxiaHu
closed
1 year ago
6
No chromosomes are in common
#110
Jason-Qiuhai
closed
1 year ago
9
coverage_norm fix for new cooltools coverage. Fixed multiprocessing for python>=3.9.13
#109
efriman
closed
1 year ago
1
Add "lib" submodule
#108
dongbohu
closed
1 year ago
1
Resolution compatibility between .cool file and .bedpe file for pile-ups of predefined regions pairs
#107
Soh-hyon
closed
1 year ago
1
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