Motif-Informed Network Inference based on Accessible Chromatin (MINI-AC) is a method that combines accessible chromatin data from bulk or single-cell experiments with transcription factor binding site enrichment to learn gene regulatory networks in plants
Update of the .gitignore file to include the correct matching for the output and error SLURM files.
Changes to give the ACR files as a channel to the genome-wide and locus-based workflows, instead of as a string/value parameter. This will make it easier to implement the changes mentioned below to include the "iCREs-based MINI-AC" feature.
Necessary script to run this "iCREs-based MINI-AC", including a process that executes a Python script to use the files with the iCREs annotated to their closest gene, to retrieve the coordinates associated with the genes of interest (input).
The input gene sets of the example to run the test of this new feature.
The corresponding example config file (and a small update on the previous one for the commented annotations, but no change to code)
The corresponding documentation update to this new feature.
Final update on the .gitignore file to avoid committing confidential files or files that are too large (iCREs BED files).
This pull request contains the following: