├── .gitattributes ├── .gitignore ├── .travis.yml ├── CHANGELOG ├── LICENSE ├── README.md ├── bin ├── epic ├── epic-blacklist ├── epic-cluster ├── epic-count ├── epic-effective ├── epic-merge ├── epic-overlaps └── epic-preprocess ├── bioconda_setup.py ├── docs ├── Makefile ├── basic_intro.rst ├── conf.py ├── epic_blacklist.rst ├── epic_cluster.rst ├── epic_count.rst ├── epic_merge.rst ├── img │ ├── epic_bigwigs.png │ ├── trunks_flanks_valleys.png │ └── trunks_flanks_valleys_counts.png ├── index.rst ├── installation.rst ├── options.rst ├── output_files.rst └── quick_start.rst ├── epic ├── __init__.py ├── bigwig │ ├── __init__.py │ └── create_bigwigs.py ├── blacklist │ ├── __init__.py │ └── compute_poisson.py ├── cluster │ ├── __init__.py │ └── cluster.py ├── config │ ├── __init__.py │ ├── constants.py │ ├── data │ │ └── hg19.chrom.sizes │ ├── genomes.py │ └── logging_settings.py ├── matrixes │ ├── __init__.py │ └── matrixes.py ├── merge │ ├── __init__.py │ ├── compute_bed_bins.py │ ├── merge.py │ └── merge_helpers.py ├── run │ ├── __init__.py │ └── run_epic.py ├── scripts │ ├── .gitignore │ ├── README.md │ ├── __init__.py │ ├── chromsizes │ │ ├── ailMel1.chromsizes │ │ ├── anoCar2.chromsizes │ │ ├── apiMel1.chromsizes │ │ ├── aplCal1.chromsizes │ │ ├── aquChr2.chromsizes │ │ ├── balAcu1.chromsizes │ │ ├── braFlo1.chromsizes │ │ ├── calJac1.chromsizes │ │ ├── calJac3.chromsizes │ │ ├── cavPor3.chromsizes │ │ ├── ce10.chromsizes │ │ ├── ce11.chromsizes │ │ ├── cerSim1.chromsizes │ │ ├── chlSab2.chromsizes │ │ ├── chrPic1.chromsizes │ │ ├── danRer10.chromsizes │ │ ├── danRer3.chromsizes │ │ ├── danRer4.chromsizes │ │ ├── danRer5.chromsizes │ │ ├── danRer6.chromsizes │ │ ├── danRer7.chromsizes │ │ ├── dm3.chromsizes │ │ ├── dm6.chromsizes │ │ ├── echTel2.chromsizes │ │ ├── equCab1.chromsizes │ │ ├── equCab2.chromsizes │ │ ├── eriEur1.chromsizes │ │ ├── eriEur2.chromsizes │ │ ├── fr1.chromsizes │ │ ├── fr2.chromsizes │ │ ├── galVar1.chromsizes │ │ ├── gasAcu1.chromsizes │ │ ├── geoFor1.chromsizes │ │ ├── gorGor3.chromsizes │ │ ├── gorGor4.chromsizes │ │ ├── gorGor5.chromsizes │ │ ├── hetGla1.chromsizes │ │ ├── hetGla2.chromsizes │ │ ├── hg18.chromsizes │ │ ├── hg19.chromsizes │ │ ├── hg38.chromsizes │ │ ├── loxAfr3.chromsizes │ │ ├── macEug2.chromsizes │ │ ├── melGal1.chromsizes │ │ ├── melGal5.chromsizes │ │ ├── micMur2.chromsizes │ │ ├── mm10.chromsizes │ │ ├── mm9.chromsizes │ │ ├── monDom4.chromsizes │ │ ├── monDom5.chromsizes │ │ ├── myoLuc2.chromsizes │ │ ├── nanPar1.chromsizes │ │ ├── nasLar1.chromsizes │ │ ├── nomLeu1.chromsizes │ │ ├── nomLeu2.chromsizes │ │ ├── nomLeu3.chromsizes │ │ ├── ochPri3.chromsizes │ │ ├── oreNil2.chromsizes │ │ ├── ornAna1.chromsizes │ │ ├── ornAna2.chromsizes │ │ ├── oryCun2.chromsizes │ │ ├── oryLat2.chromsizes │ │ ├── oviAri1.chromsizes │ │ ├── oviAri3.chromsizes │ │ ├── papAnu2.chromsizes │ │ ├── petMar1.chromsizes │ │ ├── petMar2.chromsizes │ │ ├── ponAbe2.chromsizes │ │ ├── priPac1.chromsizes │ │ ├── rheMac2.chromsizes │ │ ├── rheMac3.chromsizes │ │ ├── rheMac8.chromsizes │ │ ├── rhiRox1.chromsizes │ │ ├── rn4.chromsizes │ │ ├── rn5.chromsizes │ │ ├── rn6.chromsizes │ │ ├── sacCer1.chromsizes │ │ ├── sacCer2.chromsizes │ │ ├── sacCer3.chromsizes │ │ ├── saiBol1.chromsizes │ │ ├── sorAra2.chromsizes │ │ ├── speTri2.chromsizes │ │ ├── strPur1.chromsizes │ │ ├── strPur2.chromsizes │ │ ├── susScr2.chromsizes │ │ ├── susScr3.chromsizes │ │ ├── taeGut1.chromsizes │ │ ├── taeGut2.chromsizes │ │ ├── tarSyr2.chromsizes │ │ ├── tetNig1.chromsizes │ │ ├── tetNig2.chromsizes │ │ ├── triMan1.chromsizes │ │ ├── xenTro3.chromsizes │ │ └── xenTro7.chromsizes │ ├── effective_genome_size.py │ ├── effective_sizes │ │ ├── ailMel1_100.txt │ │ ├── ailMel1_36.txt │ │ ├── ailMel1_50.txt │ │ ├── ailMel1_75.txt │ │ ├── anoCar2_100.txt │ │ ├── anoCar2_36.txt │ │ ├── anoCar2_50.txt │ │ ├── anoCar2_75.txt │ │ ├── aplCal1_100.txt │ │ ├── aplCal1_36.txt │ │ ├── aplCal1_50.txt │ │ ├── aplCal1_75.txt │ │ ├── aquChr2_100.txt │ │ ├── aquChr2_36.txt │ │ ├── aquChr2_50.txt │ │ ├── aquChr2_75.txt │ │ ├── balAcu1_100.txt │ │ ├── balAcu1_36.txt │ │ ├── balAcu1_50.txt │ │ ├── balAcu1_75.txt │ │ ├── braFlo1_100.txt │ │ ├── braFlo1_36.txt │ │ ├── braFlo1_50.txt │ │ ├── braFlo1_75.txt │ │ ├── calJac1_100.txt │ │ ├── calJac1_36.txt │ │ ├── calJac1_50.txt │ │ ├── calJac1_75.txt │ │ ├── calJac3_100.txt │ │ ├── calJac3_36.txt │ │ ├── calJac3_50.txt │ │ ├── calJac3_75.txt │ │ ├── cavPor3_100.txt │ │ ├── cavPor3_36.txt │ │ ├── cavPor3_50.txt │ │ ├── cavPor3_75.txt │ │ ├── ce10_100.txt │ │ ├── ce10_36.txt │ │ ├── ce10_50.txt │ │ ├── ce10_75.txt │ │ ├── ce11_100.txt │ │ ├── ce11_36.txt │ │ ├── ce11_50.txt │ │ ├── ce11_75.txt │ │ ├── cerSim1_100.txt │ │ ├── cerSim1_36.txt │ │ ├── cerSim1_50.txt │ │ ├── cerSim1_75.txt │ │ ├── chlSab2_100.txt │ │ ├── chlSab2_36.txt │ │ ├── chlSab2_50.txt │ │ ├── chlSab2_75.txt │ │ ├── chrPic1_100.txt │ │ ├── chrPic1_36.txt │ │ ├── chrPic1_50.txt │ │ ├── chrPic1_75.txt │ │ ├── danRer10_100.txt │ │ ├── danRer10_36.txt │ │ ├── danRer10_50.txt │ │ ├── danRer10_75.txt │ │ ├── danRer3_100.txt │ │ ├── danRer3_36.txt │ │ ├── danRer3_50.txt │ │ ├── danRer3_75.txt │ │ ├── danRer4_100.txt │ │ ├── danRer4_36.txt │ │ ├── danRer4_50.txt │ │ ├── danRer4_75.txt │ │ ├── danRer5_100.txt │ │ ├── danRer5_36.txt │ │ ├── danRer5_50.txt │ │ ├── danRer5_75.txt │ │ ├── danRer6_100.txt │ │ ├── danRer6_36.txt │ │ ├── danRer6_50.txt │ │ ├── danRer6_75.txt │ │ ├── danRer7_100.txt │ │ ├── danRer7_36.txt │ │ ├── danRer7_50.txt │ │ ├── danRer7_75.txt │ │ ├── dm3_100.txt │ │ ├── dm3_36.txt │ │ ├── dm3_50.txt │ │ ├── dm3_75.txt │ │ ├── dm6_100.txt │ │ ├── dm6_36.txt │ │ ├── dm6_50.txt │ │ ├── dm6_75.txt │ │ ├── echTel2_100.txt │ │ ├── echTel2_36.txt │ │ ├── echTel2_50.txt │ │ ├── echTel2_75.txt │ │ ├── equCab1_100.txt │ │ ├── equCab1_36.txt │ │ ├── equCab1_50.txt │ │ ├── equCab1_75.txt │ │ ├── equCab2_100.txt │ │ ├── equCab2_36.txt │ │ ├── equCab2_50.txt │ │ ├── equCab2_75.txt │ │ ├── eriEur1_100.txt │ │ ├── eriEur1_36.txt │ │ ├── eriEur1_50.txt │ │ ├── eriEur1_75.txt │ │ ├── eriEur2_100.txt │ │ ├── eriEur2_36.txt │ │ ├── eriEur2_50.txt │ │ ├── eriEur2_75.txt │ │ ├── fr1_100.txt │ │ ├── fr1_36.txt │ │ ├── fr1_50.txt │ │ ├── fr1_75.txt │ │ ├── fr2_100.txt │ │ ├── fr2_36.txt │ │ ├── fr2_50.txt │ │ ├── fr2_75.txt │ │ ├── galVar1_100.txt │ │ ├── galVar1_36.txt │ │ ├── galVar1_50.txt │ │ ├── galVar1_75.txt │ │ ├── gasAcu1_100.txt │ │ ├── gasAcu1_36.txt │ │ ├── gasAcu1_50.txt │ │ ├── gasAcu1_75.txt │ │ ├── geoFor1_100.txt │ │ ├── geoFor1_36.txt │ │ ├── geoFor1_50.txt │ │ ├── geoFor1_75.txt │ │ ├── gorGor3_100.txt │ │ ├── gorGor3_36.txt │ │ ├── gorGor3_50.txt │ │ ├── gorGor3_75.txt │ │ ├── gorGor4_100.txt │ │ ├── gorGor4_36.txt │ │ ├── gorGor4_50.txt │ │ ├── gorGor4_75.txt │ │ ├── gorGor5_100.txt │ │ ├── gorGor5_36.txt │ │ ├── gorGor5_50.txt │ │ ├── gorGor5_75.txt │ │ ├── hetGla1_100.txt │ │ ├── hetGla1_36.txt │ │ ├── hetGla1_50.txt │ │ ├── hetGla1_75.txt │ │ ├── hetGla2_100.txt │ │ ├── hetGla2_36.txt │ │ ├── hetGla2_50.txt │ │ ├── hetGla2_75.txt │ │ ├── hg18_100.txt │ │ ├── hg18_36.txt │ │ ├── hg18_50.txt │ │ ├── hg18_75.txt │ │ ├── hg19_100.txt │ │ ├── hg19_36.txt │ │ ├── hg19_50.txt │ │ ├── hg19_75.txt │ │ ├── hg38_100.txt │ │ ├── hg38_36.txt │ │ ├── hg38_50.txt │ │ ├── hg38_75.txt │ │ ├── macEug2_100.txt │ │ ├── macEug2_36.txt │ │ ├── macEug2_50.txt │ │ ├── macEug2_75.txt │ │ ├── melGal1_100.txt │ │ ├── melGal1_36.txt │ │ ├── melGal1_50.txt │ │ ├── melGal1_75.txt │ │ ├── melGal5_100.txt │ │ ├── melGal5_36.txt │ │ ├── melGal5_50.txt │ │ ├── melGal5_75.txt │ │ ├── micMur2_100.txt │ │ ├── micMur2_36.txt │ │ ├── micMur2_50.txt │ │ ├── micMur2_75.txt │ │ ├── mm10_100.txt │ │ ├── mm10_36.txt │ │ ├── mm10_50.txt │ │ ├── mm10_75.txt │ │ ├── mm9_100.txt │ │ ├── mm9_36.txt │ │ ├── mm9_50.txt │ │ ├── mm9_75.txt │ │ ├── monDom4_100.txt │ │ ├── monDom4_36.txt │ │ ├── monDom4_50.txt │ │ ├── monDom4_75.txt │ │ ├── monDom5_100.txt │ │ ├── monDom5_36.txt │ │ ├── monDom5_50.txt │ │ ├── monDom5_75.txt │ │ ├── myoLuc2_100.txt │ │ ├── myoLuc2_36.txt │ │ ├── myoLuc2_50.txt │ │ ├── myoLuc2_75.txt │ │ ├── nanPar1_100.txt │ │ ├── nanPar1_36.txt │ │ ├── nanPar1_50.txt │ │ ├── nanPar1_75.txt │ │ ├── nasLar1_100.txt │ │ ├── nasLar1_36.txt │ │ ├── nasLar1_50.txt │ │ ├── nasLar1_75.txt │ │ ├── nomLeu1_100.txt │ │ ├── nomLeu1_36.txt │ │ ├── nomLeu1_50.txt │ │ ├── nomLeu1_75.txt │ │ ├── nomLeu2_100.txt │ │ ├── nomLeu2_36.txt │ │ ├── nomLeu2_50.txt │ │ ├── nomLeu2_75.txt │ │ ├── nomLeu3_100.txt │ │ ├── nomLeu3_36.txt │ │ ├── nomLeu3_50.txt │ │ ├── nomLeu3_75.txt │ │ ├── ochPri3_100.txt │ │ ├── ochPri3_36.txt │ │ ├── ochPri3_50.txt │ │ ├── ochPri3_75.txt │ │ ├── oreNil2_100.txt │ │ ├── oreNil2_36.txt │ │ ├── oreNil2_50.txt │ │ ├── oreNil2_75.txt │ │ ├── ornAna1_100.txt │ │ ├── ornAna1_36.txt │ │ ├── ornAna1_50.txt │ │ ├── ornAna1_75.txt │ │ ├── ornAna2_100.txt │ │ ├── ornAna2_36.txt │ │ ├── ornAna2_50.txt │ │ ├── ornAna2_75.txt │ │ ├── oryCun2_100.txt │ │ ├── oryCun2_36.txt │ │ ├── oryCun2_50.txt │ │ ├── oryCun2_75.txt │ │ ├── oryLat2_100.txt │ │ ├── oryLat2_36.txt │ │ ├── oryLat2_50.txt │ │ ├── oryLat2_75.txt │ │ ├── oviAri1_100.txt │ │ ├── oviAri1_36.txt │ │ ├── oviAri1_50.txt │ │ ├── oviAri1_75.txt │ │ ├── oviAri3_100.txt │ │ ├── oviAri3_36.txt │ │ ├── oviAri3_50.txt │ │ ├── oviAri3_75.txt │ │ ├── petMar1_100.txt │ │ ├── petMar1_36.txt │ │ ├── petMar1_50.txt │ │ ├── petMar1_75.txt │ │ ├── petMar2_100.txt │ │ ├── petMar2_36.txt │ │ ├── petMar2_50.txt │ │ ├── petMar2_75.txt │ │ ├── ponAbe2_100.txt │ │ ├── ponAbe2_36.txt │ │ ├── ponAbe2_50.txt │ │ ├── ponAbe2_75.txt │ │ ├── priPac1_100.txt │ │ ├── priPac1_36.txt │ │ ├── priPac1_50.txt │ │ ├── priPac1_75.txt │ │ ├── rheMac2_100.txt │ │ ├── rheMac2_36.txt │ │ ├── rheMac2_50.txt │ │ ├── rheMac2_75.txt │ │ ├── rheMac3_100.txt │ │ ├── rheMac3_36.txt │ │ ├── rheMac3_50.txt │ │ ├── rheMac3_75.txt │ │ ├── rheMac8_100.txt │ │ ├── rheMac8_36.txt │ │ ├── rheMac8_50.txt │ │ ├── rheMac8_75.txt │ │ ├── rhiRox1_100.txt │ │ ├── rhiRox1_36.txt │ │ ├── rhiRox1_50.txt │ │ ├── rhiRox1_75.txt │ │ ├── rn4_100.txt │ │ ├── rn4_36.txt │ │ ├── rn4_50.txt │ │ ├── rn4_75.txt │ │ ├── rn5_100.txt │ │ ├── rn5_36.txt │ │ ├── rn5_50.txt │ │ ├── rn5_75.txt │ │ ├── rn6_100.txt │ │ ├── rn6_36.txt │ │ ├── rn6_50.txt │ │ ├── rn6_75.txt │ │ ├── sacCer1_100.txt │ │ ├── sacCer1_36.txt │ │ ├── sacCer1_50.txt │ │ ├── sacCer1_75.txt │ │ ├── sacCer2_100.txt │ │ ├── sacCer2_36.txt │ │ ├── sacCer2_50.txt │ │ ├── sacCer2_75.txt │ │ ├── sacCer3_100.txt │ │ ├── sacCer3_36.txt │ │ ├── sacCer3_50.txt │ │ ├── sacCer3_75.txt │ │ ├── saiBol1_100.txt │ │ ├── saiBol1_36.txt │ │ ├── saiBol1_50.txt │ │ ├── saiBol1_75.txt │ │ ├── sorAra2_100.txt │ │ ├── sorAra2_36.txt │ │ ├── sorAra2_50.txt │ │ ├── sorAra2_75.txt │ │ ├── speTri2_100.txt │ │ ├── speTri2_36.txt │ │ ├── speTri2_50.txt │ │ ├── speTri2_75.txt │ │ ├── strPur1_100.txt │ │ ├── strPur1_36.txt │ │ ├── strPur1_50.txt │ │ ├── strPur1_75.txt │ │ ├── strPur2_100.txt │ │ ├── strPur2_36.txt │ │ ├── strPur2_50.txt │ │ ├── strPur2_75.txt │ │ ├── susScr2_100.txt │ │ ├── susScr2_36.txt │ │ ├── susScr2_50.txt │ │ ├── susScr2_75.txt │ │ ├── susScr3_100.txt │ │ ├── susScr3_36.txt │ │ ├── susScr3_50.txt │ │ ├── susScr3_75.txt │ │ ├── taeGut1_100.txt │ │ ├── taeGut1_36.txt │ │ ├── taeGut1_50.txt │ │ ├── taeGut1_75.txt │ │ ├── taeGut2_100.txt │ │ ├── taeGut2_36.txt │ │ ├── taeGut2_50.txt │ │ ├── taeGut2_75.txt │ │ ├── tarSyr2_100.txt │ │ ├── tarSyr2_36.txt │ │ ├── tarSyr2_50.txt │ │ ├── tarSyr2_75.txt │ │ ├── tetNig1_100.txt │ │ ├── tetNig1_36.txt │ │ ├── tetNig1_50.txt │ │ ├── tetNig1_75.txt │ │ ├── tetNig2_100.txt │ │ ├── tetNig2_36.txt │ │ ├── tetNig2_50.txt │ │ ├── tetNig2_75.txt │ │ ├── triMan1_100.txt │ │ ├── triMan1_36.txt │ │ ├── triMan1_50.txt │ │ ├── triMan1_75.txt │ │ ├── xenTro3_100.txt │ │ ├── xenTro3_36.txt │ │ ├── xenTro3_50.txt │ │ ├── xenTro3_75.txt │ │ ├── xenTro7_100.txt │ │ ├── xenTro7_36.txt │ │ ├── xenTro7_50.txt │ │ └── xenTro7_75.txt │ ├── genome.snakefile │ └── requirements.txt ├── src │ ├── __init__.py │ └── find_islands.pyx ├── statistics │ ├── __init__.py │ ├── add_to_island_expectations.py │ ├── add_to_island_expectations_cython.pyx │ ├── compute_background_probabilites.py │ ├── compute_poisson.py │ ├── compute_score_threshold.py │ ├── compute_values_needed_for_recurrence.py │ ├── compute_window_score.py │ ├── count_to_pvalue.py │ ├── fdr.py │ └── generate_cumulative_distribution.py ├── utils │ ├── __init__.py │ ├── find_readlength.py │ └── helper_functions.py ├── version.py └── windows │ ├── __init__.py │ ├── cluster │ ├── __init__.py │ └── find_islands.py │ └── count │ ├── __init__.py │ ├── count_reads_in_windows.py │ ├── merge_chromosome_dfs.py │ └── remove_out_of_bounds_bins.py ├── example_pipeline ├── Snakefile ├── envs │ └── macs2.yaml ├── find_regions_for_visualization.py ├── large_config.yaml └── scripts │ └── add_color_trunks_flanks_valleys_bed.py ├── examples ├── bed_to_bedpe.py ├── control.bam ├── control.bed ├── control.bedpe ├── control2.bed ├── epic-overlaps │ ├── 0h_H3K4me3.matrix │ ├── 0h_H3K4me3.regions │ ├── 0h_H3K4me3_region.matrix │ ├── 12h_H3K4me3.regions │ ├── 15h_H3K4me3.regions │ ├── 18h_H3K4me3.regions │ ├── 21h_H3K4me3.regions │ ├── 24h_H3K4me3.regions │ ├── 3h_H3K4me3.matrix │ ├── 3h_H3K4me3.regions │ ├── 3h_H3K4me3_region.matrix │ ├── 6h_H3K4me3.matrix │ ├── 6h_H3K4me3.regions │ ├── 6h_H3K4me3_region.matrix │ ├── 9h_H3K4me3.regions │ ├── nucleotide_overlap_result.csv │ └── region_overlap_result.csv ├── expected_results.csv ├── expected_results_log2fc.csv ├── genome │ └── pretend_genome.fa ├── test.bam ├── test.bed ├── test.bedpe └── test2.bed ├── helper_scripts.md ├── img └── 4C.png ├── mypy.ini ├── setup.py └── tests ├── __init__.py ├── bigwig └── test_create_bigwigs.py ├── blacklist └── test_blacklist.py ├── cluster ├── test_cluster.py └── test_create_cluster_bed.py ├── config └── test_genomes.py ├── conftest.py ├── merge ├── test_add_regions.py ├── test_compute_bed_bins.py ├── test_epic_merge.py └── test_epic_merge_with_regions.py ├── run ├── test_merge_chip_and_input.py └── test_run_epic.py ├── run_all_tests.sh ├── run_current_test.sh ├── run_integration_tests.sh ├── run_mergepool_tests.sh ├── run_script_tests.sh ├── run_slow_tests.sh ├── run_unittests.sh ├── scripts ├── test_add_color_trunks_flanks_valleys_bed.py ├── test_effective_genome_size.py ├── test_overlaps.py └── test_overlaps_nucleotides.py ├── statistics └── test_fdr.py ├── utils └── test_find_readlength.py └── windows ├── __init__.py ├── test_count_reads_in_windows.py └── test_merge_chromosome_dfs.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore-ntnu/epic/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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