New pip package? - Githubissues

hiclib / pastis

Poisson-based algorithm for stable inference of DNA Structure

http://hiclib.github.io/pastis/

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New pip package? #105

Open pierrepo opened 1 year ago

pierrepo commented 1 year ago

Dear Pastis developers,

A new paper has been published with some interesting features provided by Pastis (notably the negative binomial model). Would it be possible to, please, have a new pip package as well?

will-NYGC commented 1 year ago

Dear Pastis developers,

A new paper has been published with some interesting features provided by Pastis (notably the negative binomial model). Would it be possible to, please, have a new pip package as well?

I would also be interested in trying the negative binomial model. Any plans to include?

jinlizhang200706 commented 1 year ago

Hi pastis developer,
I'm currently trying to use this package as well. can you update the code?

gesinecauer commented 1 year ago

Hi everyone! Apologies for the delayed response. The negative binomial model described in Varoquaux et al 2023 is not yet available on PyPI, but you can still use the code. I suggest cloning this repository, then following the instructions in README.rst to install the dependencies and downloaded code.

@NelleV, can you provide instructions on running the negative binomial model?

pierrepo commented 1 year ago

For what it's worth, here is how we install Pastis-NB in our workflow:

We install pastis 0.4.0 with pip (and conda): https://github.com/data-fun/3d-genome-builder/blob/master/envs/workflow.yml
Then we clone the GitHub repo and extract the appropriate directories: https://github.com/data-fun/3d-genome-builder/blob/master/envs/workflow.post-deploy.sh