cooltools
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open2c
The tools for your .cool's
Hi, My apologies if this question sounds naive. I actually want to perform the pile ups around the centromeres in cool file that I am working with. the coordinates look...
Hello, I am relatively new to Hi-C analysis. I am currently attempting to use the dots() function as utilized in https://github.com/open2c/open2c_examples/blob/master/dots.ipynb to identify enriched points in the Hi-C contact matrix....
the first two diagonals of a contact map are often avoided for technical reasons. Default smoothing, however, does not propagate this to the .smoothed columns. We currently manually undo this...
## done ### tests - [x] set up tests/publish via Github actions! - [x] test for cli.eigs_cis passing a reference track - [x] tests for lib.checks ### checks and standards...
proposal: migrate log-smoothing code to a mini repository. https://github.com/open2c/cooltools/blob/0a7c01f9d186e36bb37cda22583e394fd0611e29/cooltools/sandbox/expected_smoothing.py#L81 why? - cooltools, pairtools, and polykit all need smoothing of contacts vs. distance but shouldn't be each other's dependencies. - each...
https://github.com/open2c/cooltools/blob/ba2be42c714fffb6b62ea13e7ecfbecb5f4a4d9a/cooltools/api/expected.py#L776 for example, standard deviation (or variance) instead of sum/mean.
https://github.com/open2c/cooltools/blob/ba2be42c714fffb6b62ea13e7ecfbecb5f4a4d9a/cooltools/cli/expected_cis.py#L46 issue: currently API returns smoothed & aggregated by default, but CLI does not. proposal: CLI should smooth and aggregate across regions by default. After addressing this issue, a release...
Should we return scores as NaN for bins within a window size of regions start/ends? https://github.com/open2c/cooltools/blob/ba2be42c714fffb6b62ea13e7ecfbecb5f4a4d9a/cooltools/api/insulation.py#L495
Hi There, I am attempting to call cooltools.api.snipping.pileup(clr,features_df=peak_df , flank=300_000), where : peak_df = pd.read_csv(f"ctcf.enhancer.promoters/{peak}.bed", sep="\t", names=['chrom', "start", "end"]), as per the cooltools feature_df requirements. I am not passing in...
