coolpuppy

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[Q] Setting --mindist parameter as 0, but not contain all number of loop(input loop.bedpe)

3

**State the question** A clear and concise description of the question. **What have you tried?** - [√ ] Have you read the documentation and tutorials about your question? **Additional context**...

Miracle-Yao

To access a value by position, use `ser.iloc[pos]` chroffset = self.clr.offset(region[0])

2

Hi, dear authors, I have used coolpup a lot previously, but recently it has some problem(maybe a version problem of some packages): coolpup.py aa.cool bb.bed --outname cc.txt --flank 250000 --local...

jiangshan529

Extracting locus strength scores for loops

3

Hello, I'm doing aggregate loop analysis and I was wondering if you have something like [this](https://coolpuppy.readthedocs.io/en/latest/Examples/TAD_score.html) for loops? I'm not very well versed in python, but will try on my...

NMaziak

Hi, Thank you so much for providing this program it is very useful ! I performed HiC experiment and process the sequencing raw data using Juicer (.hic) and Hicexplorer (.h5...

Lucas446

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

2

Hi, thank you for helping with previous issue. after running the coolpup coolpup.py $FOLDER/file.cool --outname $FOLDER/file.cool_out $FOLDER/encode_chipseq.bed I ve get a cool_out file which is quite small in size (attached...

odovgusha

`pu.pileupsWithControl` might skip some pile-up regions or raise vague `domain_score not in dict2` AssertionError

1

Hi, I bumped into some unclear behavior of coolpup.py. Finally, I managed to overcome the problem, but maybe this issue might be helpful for other users and might help to...

nvaulin

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

4

I received the following error: `TypeError: unsupported operand type(s) for +: 'int' and 'str'` when I execute the following code `pup_MT = coolpup.pileup(clr_MT, df_arm_p_pairs, features_format='bedpe', trans=True, expected_df=trans_expected_MT, flank = 50000,...

ratheraarif

[Q]Understanding rescaling

1

I am looking at the rescaling example in the notebook and have the following questions: 1. Where is the pile up plot centered? The example looks like it's centered at...

zhaoyycrow

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

1

**State the question** I generated a set of pileups, all using the same list of regions, but with different Hi-C files. How do I test if the resulting pileups are...

AudreyBaguette