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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Function to find common peaks between two .bed files #105

Closed salwanbutrus closed 1 year ago

salwanbutrus commented 1 year ago

Is your feature request related to a problem? Please describe. I have one dataset. I performed peak calling on it two ways, so now I have two different consensus_peaks.bed files. I would like to compare the two peak sets.

Describe the solution you'd like Are there tools in SCENIC+ to compare these two files? For example, to find intersecting peaks given some X bp window.

Describe alternatives you've considered Here is an example from Signac in R, but I was wondering if SCENIC+ contains any tools.

Thank you for your time! Salwan

SeppeDeWinter commented 1 year ago

Hi @salwanbutrus

Not specifically in SCENIC+ but you can use pyranges for this.

Best,

Seppe

salwanbutrus commented 1 year ago

Thank you!

On Thu, Feb 9, 2023 at 11:51 PM Seppe @.***> wrote:

Hi @salwanbutrus https://github.com/salwanbutrus

Not specifically in SCENIC+ but you can use pyranges https://pyranges.readthedocs.io/en/latest/autoapi/pyranges/index.html for this.

Best,

Seppe

— Reply to this email directly, view it on GitHub https://github.com/aertslab/scenicplus/issues/105#issuecomment-1425347462, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKMHFVXD6OFON2CXGCO4YITWWXXO7ANCNFSM6AAAAAAUV2JKCE . You are receiving this because you were mentioned.Message ID: @.***>

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Salwan ButrusPhD Candidate | Chemical and Biomolecular Engineering UC Berkeley Mobile Phone: 248-778-8740 Website https://salwanbutrus.github.io/ | Twitter https://twitter.com/salwan_butrus

SeppeDeWinter commented 1 year ago

You're welcome