├── .gitignore ├── DOCKER_FILE_HAYSTACK ├── LICENSE ├── MANIFEST.in ├── README.md ├── dependencies ├── Darwin │ └── dep_here ├── Linux │ └── dep_here └── dep_here ├── extra ├── PeakAnnotator.jar ├── logo.css ├── logo.pm ├── seqlogo ├── template.eps ├── template.pm └── templates │ ├── haystack_logo.png │ ├── noise.png │ └── report_template.html ├── gene_annotations ├── bosTau7_genes.bed ├── bosTau7_genes_id_to_names ├── galGal4_genes.bed ├── galGal4_genes_id_to_names ├── hg19_genes.bed ├── hg19_genes_id_to_names ├── hg38_genes.bed ├── hg38_genes_id_to_names ├── mm10_genes.bed ├── mm10_genes_id_to_names ├── mm9_genes.bed └── mm9_genes_id_to_names ├── genomes └── put_here_the_genomes_from_ucsc ├── haystack ├── __init__.py ├── bioutilities.py ├── external.py ├── haystack_common.py ├── haystack_download_genome_CORE.py ├── haystack_hotspots_CORE.py ├── haystack_motifs_CORE.py ├── haystack_pipeline_CORE.py └── haystack_tf_activity_plane_CORE.py ├── haystack_download_genome.py ├── haystack_hotspots.py ├── haystack_motifs.py ├── haystack_pipeline.py ├── motif_databases ├── FACTORBOOK.meme ├── FACTORBOOK_mapped_to_gene_human_mouse.txt ├── JASPAR_CORE_2014_vertebrates.meme ├── JASPAR_CORE_2014_vertebrates_mapped_to_chicken.txt ├── JASPAR_CORE_2014_vertebrates_mapped_to_cow.txt ├── JASPAR_CORE_2014_vertebrates_mapped_to_gene_human_mouse.txt ├── JASPAR_CORE_2016_vertebrates.meme ├── JASPAR_CORE_2016_vertebrates_mapped_to_gene_human_mouse.txt ├── JASPAR_CORE_REDUNDANT_2016_vertebrates.meme ├── JASPAR_CORE_REDUNDANT_2016_vertebrates_mapped_to_gene_human_mouse.txt └── MAP_MOTIFS_TO_GENES.ipynb ├── precompiled_binary ├── Darwin │ ├── bedGraphToBigWig │ └── bigWigAverageOverBed └── Linux │ ├── bedGraphToBigWig │ └── bigWigAverageOverBed ├── setup.cfg ├── setup.py └── test_bed ├── Background_for_H1hesc_H3k27ac.bed ├── Regions_specific_for_H1hesc_H3k27ac.bed └── test_haystack_motifs.sh /.gitignore: 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