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README.md -
bin/1.1_footprint_extraction/footprints_extraction.py -
bin/1.2_filter_motifs/compareBed.sh -
bin/1.2_filter_motifs/maxScore.R -
bin/1.2_filter_motifs/merge.R -
bin/1.2_filter_motifs/tfbsscan.py -
bin/2.1_clustering/cdhit_wrapper.R -
bin/2.1_clustering/reduce_sequence.R -
bin/2.2_motif_estimation/bed_to_fasta.R -
bin/2.2_motif_estimation/get_best_motif.py -
bin/2.2_motif_estimation/label_cluster.R -
bin/2.2_motif_estimation/merge_similar_clusters.R -
bin/2.2_motif_estimation/motif_estimation.nf -
bin/3.1_create_gtf/Modules/CrossMap.py -
bin/3.1_create_gtf/Modules/CrossMapper.py -
bin/3.1_create_gtf/Modules/Ensembl/ActivityCategorizer.py -
bin/3.1_create_gtf/Modules/Ensembl/ActivityTable.py -
bin/3.1_create_gtf/Modules/Ensembl/ActivityTableGenerator.py -
bin/3.1_create_gtf/Modules/Ensembl/Ensembl.py -
bin/3.1_create_gtf/Modules/Ensembl/FTPHandling/FTPEntry.py -
bin/3.1_create_gtf/Modules/Ensembl/FTPHandling/URLRetrieve.py -
bin/3.1_create_gtf/Modules/Ensembl/FTPHandling/VersionChecker.py -
bin/3.1_create_gtf/Modules/Ensembl/FTPHandling/__init__.py -
bin/3.1_create_gtf/Modules/Ensembl/FTPHandling/__pycache__/FTPEntry.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/FTPHandling/__pycache__/URLRetrieve.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/FTPHandling/__pycache__/VersionChecker.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/FTPHandling/__pycache__/__init__.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py -
bin/3.1_create_gtf/Modules/Ensembl/__init__.py -
bin/3.1_create_gtf/Modules/Ensembl/__pycache__/ActivityCategorizer.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/__pycache__/ActivityTable.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/__pycache__/ActivityTableGenerator.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/__pycache__/Ensembl.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/__pycache__/GTFGen.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/__pycache__/__init__.cpython-35.pyc -
bin/3.1_create_gtf/Modules/Ensembl/checksums.py -
bin/3.1_create_gtf/Modules/SaveResults.py -
bin/3.1_create_gtf/Modules/Uniquifier.py -
bin/3.1_create_gtf/Modules/__init__.py -
bin/3.1_create_gtf/Modules/__pycache__/CrossMap.cpython-35.pyc -
bin/3.1_create_gtf/Modules/__pycache__/CrossMapper.cpython-35.pyc -
bin/3.1_create_gtf/Modules/__pycache__/SaveResults.cpython-35.pyc -
bin/3.1_create_gtf/Modules/__pycache__/Uniquifier.cpython-35.pyc -
bin/3.1_create_gtf/Modules/__pycache__/__init__.cpython-35.pyc -
bin/3.1_create_gtf/Modules/ucsc/__init__.py -
bin/3.1_create_gtf/Modules/ucsc/__pycache__/__init__.cpython-35.pyc -
bin/3.1_create_gtf/Modules/ucsc/__pycache__/ucsc.cpython-35.pyc -
bin/3.1_create_gtf/Modules/ucsc/bigBedToBed -
bin/3.1_create_gtf/Modules/ucsc/ucsc.py -
bin/3.1_create_gtf/RegGTFExtractor.py -
bin/3.1_create_gtf/config/celltypes_homo_sapiens.json -
bin/3.1_create_gtf/config/celltypes_mus_musculus.json -
bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/CHECKSUMS -
bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/activity/A549/CHECKSUMS -
bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/activity/A549/homo_sapiens.GRCh38.A549.Regulatory_Build.regulatory_activity.20161111.gff.gz -
bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/activity/Aorta/CHECKSUMS -
bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/activity/Aorta/homo_sapiens.GRCh38.Aorta.Regulatory_Build.regulatory_activity.20161111.gff.gz -
bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/homo_sapiens.GRCh38.Regulatory_Build.regulatory_features.20161111.gff.gz -
bin/3.1_create_gtf/data/UCSCData/hg38.bed -
config/cluster.config -
config/create_gtf.config -
config/filter_unknown_motifs.config -
config/motif_estimation.config -
config/peak_calling.config -
config/uropa.config -
masterenv.yml -
nextflow.config -
pipeline.nf