├── .gitattributes ├── .github └── workflows │ └── stale.yml ├── .gitignore ├── CHANGES ├── LICENSE ├── MANIFEST.in ├── README.md ├── figures ├── BATF_footprint_comparison_all.png ├── BATF_footprint_comparison_subsets.png ├── BATF_heatmap.png ├── IRF1_footprint.png ├── atacorrect.png ├── bindetect.png ├── chr4-119628321-119629356.png ├── chr4-163701830-163702617.png ├── footprinting.png ├── network.png └── tobias.png ├── pyproject.toml ├── setup.py ├── tobias ├── TOBIAS.py ├── __init__.py ├── parsers.py ├── scripts │ ├── S3_Downloader.py │ ├── TFs2genesOfInterest.sh │ ├── cluster_sites_by_overlap.py │ ├── filter_important_factors.py │ └── s3_tobias_data_config.yaml ├── tools │ ├── __init__.py │ ├── atacorrect.py │ ├── atacorrect_functions.py │ ├── bindetect.py │ ├── bindetect_functions.py │ ├── cluster_tfbs.py │ ├── create_network.py │ ├── download_data.py │ ├── filter_fragments.py │ ├── format_motifs.py │ ├── log2table.py │ ├── maxpos.py │ ├── merge_pdfs.py │ ├── motif_clust.py │ ├── plot_aggregate.py │ ├── plot_changes.py │ ├── plot_heatmap.py │ ├── plot_tracks.py │ ├── score_bed.py │ ├── score_bigwig.py │ ├── submerge.py │ ├── subsample_bam.py │ └── tfbscan.py └── utils │ ├── __init__.py │ ├── logger.py │ ├── motifs.py │ ├── ngs.pyx │ ├── regions.py │ ├── sequences.pyx │ ├── signals.pyx │ └── utilities.py └── tobias_env.yaml /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loosolab/TOBIAS/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/stale.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loosolab/TOBIAS/HEAD/.github/workflows/stale.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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