feather-creator 0.0.3

motif-TG .feather files creation and motifs-TF mapping from a list

feather_creator

Allows creation of .feather file to use in the pyscenic pipeline from motifs and gene sequences.

Dependencies

• pip install numpy version 1.19.5
• pip install biopython version 1.73
• pip install pyarrow version 0.16.0
• pip install pandas
• pip install tqdm

using pip environment

• python3 -m venv feather_creator_env
• source feather_creator_env/bin/activate
• python3 -m pip install -r requirements.txt

Installation:

TODO : ajouter sur pypi pip install feather_creator

Tutorials:

Material

This module relies on the iRegulon dataset, which has also been used for i-cistarget.

http://iregulon.aertslab.org/collections.html#motifcolldownload

Direct download link for the motif collection:

https://resources.aertslab.org/papers/iregulon/motifColl-10k-all-public.tar.gz

(Janky and Verfaillie et al., PLoS Comp Biol 2014)

Necessary motif-TF association file:

https://resources.aertslab.org/cistarget/motif2tf/