motif-TG .feather files creation and motifs-TF mapping from a list
Project description
feather_creator
Allows creation of .feather file to use in the pyscenic pipeline from motifs and gene sequences.
Dependencies
pip install numpy
version 1.19.5pip install biopython
version 1.73pip install pyarrow
version 0.16.0pip 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:
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