.codeclimate.yml
.pre-commit-config.yaml
.rtd-environment.yml
.travis.yml
CHANGELOG.md
CITATION.cff
COPYING
INSTALL
MANIFEST.in
README.md
compile_externals.py
conda_env.dev.txt
conda_env.osx.txt
conda_env.test.txt
conda_env.txt
readthedocs.yml
requirements.txt
setup.cfg
setup.py
versioneer.py
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/other.md
binder/environment.yml
data/__init__.py
data/test.develop.out
data/bg/hg18.MotifSampler.bg
data/bg/hg19.MotifSampler.bg
data/bg/hg38.MotifSampler.bg
data/bg/mm10.MotifSampler.bg
data/bg/mm9.MotifSampler.bg
data/bg/xenTro2.MotifSampler.bg
data/cfg/gimmemotifs.default.cfg
data/examples/Gm12878.CTCF.top500.w200.fa
data/examples/MA0099.3.jaspar
data/examples/TAp73alpha.bed
data/examples/TAp73alpha.fa
data/examples/example.pfm
data/examples/test.small.fa
data/motif_databases/CIS-BP.motif2factors.txt
data/motif_databases/CIS-BP.pfm
data/motif_databases/ENCODE.motif2factors.txt
data/motif_databases/ENCODE.pfm
data/motif_databases/HOCOMOCOv10_HUMAN.motif2factors.txt
data/motif_databases/HOCOMOCOv10_HUMAN.pfm
data/motif_databases/HOCOMOCOv10_MOUSE.motif2factors.txt
data/motif_databases/HOCOMOCOv10_MOUSE.pfm
data/motif_databases/HOCOMOCOv11_HUMAN.motif2factors.txt
data/motif_databases/HOCOMOCOv11_HUMAN.pfm
data/motif_databases/HOCOMOCOv11_MOUSE.motif2factors.txt
data/motif_databases/HOCOMOCOv11_MOUSE.pfm
data/motif_databases/HOMER.motif2factors.txt
data/motif_databases/HOMER.pfm
data/motif_databases/IMAGE.motif2factors.txt
data/motif_databases/IMAGE.pfm
data/motif_databases/JASPAR2018.motif2factors.txt
data/motif_databases/JASPAR2018.pfm
data/motif_databases/JASPAR2018_fungi.motif2factors.txt
data/motif_databases/JASPAR2018_fungi.pfm
data/motif_databases/JASPAR2018_insects.motif2factors.txt
data/motif_databases/JASPAR2018_insects.pfm
data/motif_databases/JASPAR2018_nematodes.motif2factors.txt
data/motif_databases/JASPAR2018_nematodes.pfm
data/motif_databases/JASPAR2018_plants.motif2factors.txt
data/motif_databases/JASPAR2018_plants.pfm
data/motif_databases/JASPAR2018_urochordates.motif2factors.txt
data/motif_databases/JASPAR2018_urochordates.pfm
data/motif_databases/JASPAR2018_vertebrates.motif2factors.txt
data/motif_databases/JASPAR2018_vertebrates.pfm
data/motif_databases/JASPAR2020.motif2factors.txt
data/motif_databases/JASPAR2020.pfm
data/motif_databases/JASPAR2020_fungi.motif2factors.txt
data/motif_databases/JASPAR2020_fungi.pfm
data/motif_databases/JASPAR2020_insects.motif2factors.txt
data/motif_databases/JASPAR2020_insects.pfm
data/motif_databases/JASPAR2020_nematodes.motif2factors.txt
data/motif_databases/JASPAR2020_nematodes.pfm
data/motif_databases/JASPAR2020_plants.motif2factors.txt
data/motif_databases/JASPAR2020_plants.pfm
data/motif_databases/JASPAR2020_urochordates.motif2factors.txt
data/motif_databases/JASPAR2020_urochordates.pfm
data/motif_databases/JASPAR2020_vertebrates.motif2factors.txt
data/motif_databases/JASPAR2020_vertebrates.pfm
data/motif_databases/JASPAR2022.motif2factors.txt
data/motif_databases/JASPAR2022.pfm
data/motif_databases/JASPAR2022_fungi.motif2factors.txt
data/motif_databases/JASPAR2022_fungi.pfm
data/motif_databases/JASPAR2022_insects.motif2factors.txt
data/motif_databases/JASPAR2022_insects.pfm
data/motif_databases/JASPAR2022_nematodes.motif2factors.txt
data/motif_databases/JASPAR2022_nematodes.pfm
data/motif_databases/JASPAR2022_plants.motif2factors.txt
data/motif_databases/JASPAR2022_plants.pfm
data/motif_databases/JASPAR2022_urochordates.motif2factors.txt
data/motif_databases/JASPAR2022_urochordates.pfm
data/motif_databases/JASPAR2022_vertebrates.motif2factors.txt
data/motif_databases/JASPAR2022_vertebrates.pfm
data/motif_databases/RSAT_insects.motif2factors.txt
data/motif_databases/RSAT_insects.pfm
data/motif_databases/RSAT_plants.motif2factors.txt
data/motif_databases/RSAT_plants.pfm
data/motif_databases/RSAT_vertebrates.motif2factors.txt
data/motif_databases/RSAT_vertebrates.pfm
data/motif_databases/SwissRegulon.motif2factors.txt
data/motif_databases/SwissRegulon.pfm
data/motif_databases/factorbook.motif2factors.txt
data/motif_databases/factorbook.pfm
data/motif_databases/gimme.invertebrate.v1.0.pwm
data/motif_databases/gimme.plant.v1.0.pwm
data/motif_databases/gimme.vertebrate.v3.1.factor2motifs.txt
data/motif_databases/gimme.vertebrate.v3.1.motif2factors.txt
data/motif_databases/gimme.vertebrate.v3.1.pwm
data/motif_databases/gimme.vertebrate.v5.0.motif2factors.txt
data/motif_databases/gimme.vertebrate.v5.0.pfm
data/score_dists/dic2_bg_mean_sd.txt
data/score_dists/dic2_mean_sd.txt
data/score_dists/total_wic_mean_score_dist.txt
data/templates/cluster_template.jinja.html
data/templates/report_template.jinja.html
data/templates/star.png
data/templates/star_silver.png
data/templates/table.tpl
data/templates/sortable/sortable-theme-slick.css
data/templates/sortable/sortable.min.js
docs/Makefile
docs/acknowledgments.rst
docs/api.rst
docs/conf.py
docs/examples.rst
docs/faq.rst
docs/index.rst
docs/installation.rst
docs/overview.rst
docs/reference.rst
docs/release_checklist.md
docs/requirements.txt
docs/tutorials.rst
docs/gimme.CTCF/combined.motif2factors.txt
docs/gimme.CTCF/combined.pfm
docs/gimme.CTCF/gimme.denovo.clusters.html
docs/gimme.CTCF/gimme.denovo.html
docs/gimme.CTCF/gimme.denovo.pfm
docs/gimme.CTCF/gimme.motifs.html
docs/gimme.CTCF/gimme.motifs.redundant.html
docs/gimme.CTCF/gimme.roc.report.txt
docs/gimme.CTCF/gimmemotifs.log
docs/gimme.CTCF/params.txt
docs/gimme.CTCF/stats.gc.txt
docs/gimme.CTCF/images/Average_53.png
docs/gimme.CTCF/images/Average_62.png
docs/gimme.CTCF/images/Average_63.png
docs/gimme.CTCF/images/Average_64.png
docs/gimme.CTCF/images/Average_65.png
docs/gimme.CTCF/images/GM.5.0.C2H2_ZF.0024.png
docs/gimme.CTCF/images/GM.5.0.C2H2_ZF.0199.png
docs/gimme.CTCF/images/GM.5.0.C2H2_ZF.0243.png
docs/gimme.CTCF/images/GM.5.0.C2H2_ZF.0254.png
docs/gimme.CTCF/images/GM.5.0.C2H2_ZF.0283.png
docs/gimme.CTCF/images/GM.5.0.HSF.0009.png
docs/gimme.CTCF/images/GM.5.0.Mixed.0079.png
docs/gimme.CTCF/images/GM.5.0.Mixed.0096.png
docs/gimme.CTCF/images/GM.5.0.Mixed.0100.png
docs/gimme.CTCF/images/GM.5.0.THAP_finger.0005.png
docs/gimme.CTCF/images/GM.5.0.Unknown.0031.png
docs/gimme.CTCF/images/GM.5.0.Unknown.0183.png
docs/gimme.CTCF/images/GM.5.0.bZIP.0032.png
docs/gimme.CTCF/images/GimmeMotifs_1.png
docs/gimme.CTCF/images/GimmeMotifs_10.png
docs/gimme.CTCF/images/GimmeMotifs_10_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_10_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_11.png
docs/gimme.CTCF/images/GimmeMotifs_11_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_11_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_12.png
docs/gimme.CTCF/images/GimmeMotifs_12_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_12_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_13.png
docs/gimme.CTCF/images/GimmeMotifs_13_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_13_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_14.png
docs/gimme.CTCF/images/GimmeMotifs_14_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_14_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_1_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_1_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_2.png
docs/gimme.CTCF/images/GimmeMotifs_2_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_2_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_3.png
docs/gimme.CTCF/images/GimmeMotifs_3_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_3_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_4.png
docs/gimme.CTCF/images/GimmeMotifs_4_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_4_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_5.png
docs/gimme.CTCF/images/GimmeMotifs_5_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_5_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_6.png
docs/gimme.CTCF/images/GimmeMotifs_6_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_6_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_7.png
docs/gimme.CTCF/images/GimmeMotifs_7_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_7_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_8.png
docs/gimme.CTCF/images/GimmeMotifs_8_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_8_roc.gc.png
docs/gimme.CTCF/images/GimmeMotifs_9.png
docs/gimme.CTCF/images/GimmeMotifs_9_histogram.svg
docs/gimme.CTCF/images/GimmeMotifs_9_roc.gc.png
docs/gimme.CTCF/images/gimme_101_MEME_1_w16.png
docs/gimme.CTCF/images/gimme_103_MEME_3_w16.png
docs/gimme.CTCF/images/gimme_10_Homer_8_5.png
docs/gimme.CTCF/images/gimme_111_MEME_1_w12.png
docs/gimme.CTCF/images/gimme_113_MEME_3_w12.png
docs/gimme.CTCF/images/gimme_11_Homer_10_1.png
docs/gimme.CTCF/images/gimme_121_MEME_1_w14.png
docs/gimme.CTCF/images/gimme_123_MEME_3_w14.png
docs/gimme.CTCF/images/gimme_12_Homer_10_2.png
docs/gimme.CTCF/images/gimme_131_MEME_1_w10.png
docs/gimme.CTCF/images/gimme_133_MEME_3_w10.png
docs/gimme.CTCF/images/gimme_13_Homer_10_3.png
docs/gimme.CTCF/images/gimme_141_MEME_1_w8.png
docs/gimme.CTCF/images/gimme_145_MEME_5_w8.png
docs/gimme.CTCF/images/gimme_149_MEME_9_w8.png
docs/gimme.CTCF/images/gimme_14_Homer_10_4.png
docs/gimme.CTCF/images/gimme_152_MEME_2_w6.png
docs/gimme.CTCF/images/gimme_16_Homer_12_1.png
docs/gimme.CTCF/images/gimme_17_Homer_12_2.png
docs/gimme.CTCF/images/gimme_1_Homer_6_1.png
docs/gimme.CTCF/images/gimme_21_BioProspector_w6_1.png
docs/gimme.CTCF/images/gimme_22_BioProspector_w6_2.png
docs/gimme.CTCF/images/gimme_24_BioProspector_w6_4.png
docs/gimme.CTCF/images/gimme_25_BioProspector_w6_5.png
docs/gimme.CTCF/images/gimme_26_BioProspector_w8_1.png
docs/gimme.CTCF/images/gimme_27_BioProspector_w8_2.png
docs/gimme.CTCF/images/gimme_28_BioProspector_w8_3.png
docs/gimme.CTCF/images/gimme_29_BioProspector_w8_4.png
docs/gimme.CTCF/images/gimme_2_Homer_6_2.png
docs/gimme.CTCF/images/gimme_30_BioProspector_w8_5.png
docs/gimme.CTCF/images/gimme_31_BioProspector_w10_1.png
docs/gimme.CTCF/images/gimme_32_BioProspector_w10_2.png
docs/gimme.CTCF/images/gimme_33_BioProspector_w10_3.png
docs/gimme.CTCF/images/gimme_34_BioProspector_w10_4.png
docs/gimme.CTCF/images/gimme_35_BioProspector_w10_5.png
docs/gimme.CTCF/images/gimme_36_BioProspector_w12_1.png
docs/gimme.CTCF/images/gimme_37_BioProspector_w12_2.png
docs/gimme.CTCF/images/gimme_38_BioProspector_w12_3.png
docs/gimme.CTCF/images/gimme_39_BioProspector_w12_4.png
docs/gimme.CTCF/images/gimme_3_Homer_6_3.png
docs/gimme.CTCF/images/gimme_40_BioProspector_w12_5.png
docs/gimme.CTCF/images/gimme_41_BioProspector_w14_1.png
docs/gimme.CTCF/images/gimme_42_BioProspector_w14_2.png
docs/gimme.CTCF/images/gimme_43_BioProspector_w14_3.png
docs/gimme.CTCF/images/gimme_44_BioProspector_w14_4.png
docs/gimme.CTCF/images/gimme_45_BioProspector_w14_5.png
docs/gimme.CTCF/images/gimme_46_BioProspector_w16_1.png
docs/gimme.CTCF/images/gimme_47_BioProspector_w16_2.png
docs/gimme.CTCF/images/gimme_48_BioProspector_w16_3.png
docs/gimme.CTCF/images/gimme_49_BioProspector_w16_4.png
docs/gimme.CTCF/images/gimme_4_Homer_6_4.png
docs/gimme.CTCF/images/gimme_50_BioProspector_w16_5.png
docs/gimme.CTCF/images/gimme_51_BioProspector_w18_1.png
docs/gimme.CTCF/images/gimme_52_BioProspector_w18_2.png
docs/gimme.CTCF/images/gimme_53_BioProspector_w18_3.png
docs/gimme.CTCF/images/gimme_54_BioProspector_w18_4.png
docs/gimme.CTCF/images/gimme_55_BioProspector_w18_5.png
docs/gimme.CTCF/images/gimme_56_BioProspector_w20_1.png
docs/gimme.CTCF/images/gimme_57_BioProspector_w20_2.png
docs/gimme.CTCF/images/gimme_58_BioProspector_w20_3.png
docs/gimme.CTCF/images/gimme_59_BioProspector_w20_4.png
docs/gimme.CTCF/images/gimme_5_Homer_6_5.png
docs/gimme.CTCF/images/gimme_60_BioProspector_w20_5.png
docs/gimme.CTCF/images/gimme_61_Homer_14_1.png
docs/gimme.CTCF/images/gimme_66_Homer_16_1.png
docs/gimme.CTCF/images/gimme_67_Homer_16_2.png
docs/gimme.CTCF/images/gimme_68_Homer_16_3.png
docs/gimme.CTCF/images/gimme_6_Homer_8_1.png
docs/gimme.CTCF/images/gimme_71_Homer_20_1.png
docs/gimme.CTCF/images/gimme_72_Homer_20_2.png
docs/gimme.CTCF/images/gimme_76_Homer_18_1.png
docs/gimme.CTCF/images/gimme_7_Homer_8_2.png
docs/gimme.CTCF/images/gimme_80_Homer_18_5.png
docs/gimme.CTCF/images/gimme_81_MEME_1_w18.png
docs/gimme.CTCF/images/gimme_83_MEME_3_w18.png
docs/gimme.CTCF/images/gimme_8_Homer_8_3.png
docs/gimme.CTCF/images/gimme_91_MEME_1_w20.png
docs/gimme.CTCF/images/gimme_93_MEME_3_w20.png
docs/gimme.CTCF/images/gimme_9_Homer_8_4.png
docs/gimme.CTCF/images/star.png
docs/gimme.CTCF/logos/GimmeMotifs_1.png
docs/gimme.CTCF/logos/GimmeMotifs_10.png
docs/gimme.CTCF/logos/GimmeMotifs_11.png
docs/gimme.CTCF/logos/GimmeMotifs_13.png
docs/gimme.CTCF/logos/GimmeMotifs_14.png
docs/gimme.CTCF/logos/GimmeMotifs_2.png
docs/gimme.CTCF/logos/GimmeMotifs_3.png
docs/gimme.CTCF/logos/GimmeMotifs_4.png
docs/gimme.CTCF/logos/GimmeMotifs_5.png
docs/gimme.CTCF/logos/GimmeMotifs_6.png
docs/gimme.CTCF/logos/GimmeMotifs_8.png
docs/images/GM.5.0.Grainyhead.0001.png
docs/images/GM.5.0.p53.0001.png
docs/images/GM.5.0.p53.0004.png
docs/images/MA1115.1_POU5F1.energy.notitle.png
docs/images/MA1115.1_POU5F1.energy.png
docs/images/MA1115.1_POU5F1.ensembl.png
docs/images/MA1115.1_POU5F1.frequency.png
docs/images/MA1115.1_POU5F1.information.png
docs/images/ap1.png
docs/images/gimme.maelstrom.report.png
docs/images/gimme.motifs.known.report.png
docs/images/gimme_diff_tbox.png
docs/images/heatmap.png
docs/notebooks/api_examples.ipynb
gimmemotifs/__init__.py
gimmemotifs/_version.py
gimmemotifs/background.py
gimmemotifs/c_metrics.c
gimmemotifs/cli.py
gimmemotifs/cluster.py
gimmemotifs/comparison.py
gimmemotifs/config.py
gimmemotifs/denovo.py
gimmemotifs/fasta.py
gimmemotifs/maelstrom.py
gimmemotifs/moap.py
gimmemotifs/orthologs.py
gimmemotifs/plot.py
gimmemotifs/prediction.py
gimmemotifs/preprocessing.py
gimmemotifs/rank.py
gimmemotifs/report.py
gimmemotifs/rocmetrics.py
gimmemotifs/scanner.py
gimmemotifs/shutils.py
gimmemotifs/stats.py
gimmemotifs/utils.fix.py
gimmemotifs/utils.py
gimmemotifs/validation.py
gimmemotifs.egg-info/PKG-INFO
gimmemotifs.egg-info/SOURCES.txt
gimmemotifs.egg-info/dependency_links.txt
gimmemotifs.egg-info/requires.txt
gimmemotifs.egg-info/top_level.txt
gimmemotifs/commands/__init__.py
gimmemotifs/commands/background.py
gimmemotifs/commands/cluster.py
gimmemotifs/commands/diff.py
gimmemotifs/commands/location.py
gimmemotifs/commands/logo.py
gimmemotifs/commands/maelstrom.py
gimmemotifs/commands/match.py
gimmemotifs/commands/motif2factors.py
gimmemotifs/commands/motifs.py
gimmemotifs/commands/pfmscan.py
gimmemotifs/commands/prediction.py
gimmemotifs/commands/threshold.py
gimmemotifs/db/__init__.py
gimmemotifs/included_tools/__init__.py
gimmemotifs/motif/__init__.py
gimmemotifs/motif/_comparison.py
gimmemotifs/motif/_plotting.py
gimmemotifs/motif/_scanning.py
gimmemotifs/tools/__init__.py
gimmemotifs/tools/amd.py
gimmemotifs/tools/bioprospector.py
gimmemotifs/tools/chipmunk.py
gimmemotifs/tools/dinamo.py
gimmemotifs/tools/dreme.py
gimmemotifs/tools/gadem.py
gimmemotifs/tools/hms.py
gimmemotifs/tools/homer.py
gimmemotifs/tools/improbizer.py
gimmemotifs/tools/jaspar.py
gimmemotifs/tools/mdmodule.py
gimmemotifs/tools/meme.py
gimmemotifs/tools/memew.py
gimmemotifs/tools/motifprogram.py
gimmemotifs/tools/motifsampler.py
gimmemotifs/tools/posmo.py
gimmemotifs/tools/prosampler.py
gimmemotifs/tools/rpmcmc.py
gimmemotifs/tools/trawler.py
gimmemotifs/tools/weeder.py
gimmemotifs/tools/xxmotif.py
gimmemotifs/tools/yamda.py
scripts/combine_peaks
scripts/coverage_table
scripts/download_motif_databases.py
scripts/gimme
scripts/gimme_benchmark
src/COPYING
src/README
src/AMD/AMD.bin
src/BioProspector/BioProspector
src/BioProspector/BioProspector.c
src/BioProspector/COPYING
src/ChIPMunk/ChIPMunk.sh
src/ChIPMunk/chipmunk.jar
src/HMS/hms
src/HMS/theta0.txt
src/HMS/theta1.txt
src/HMS/theta2.txt
src/HMS/theta3.txt
src/Improbizer/ameme_i386
src/Improbizer/ameme_x86_64
src/MDmodule/COPYING
src/MDmodule/MDmodule
src/MDmodule/MDmodule.c
src/MotifSampler/CreateBackgroundModel_i386
src/MotifSampler/CreateBackgroundModel_x86_64
src/MotifSampler/MotifSampler_i386
src/MotifSampler/MotifSampler_x86_64
src/posmo/clusterwd
src/posmo/posmo
test/test.py
test/test_01_setup.py
test/test_background.py
test/test_cli.py
test/test_cluster.py
test/test_comparison.py
test/test_denovo.py
test/test_fasta.py
test/test_maelstrom.py
test/test_metrics.py
test/test_moap.py
test/test_motif.py
test/test_motif_databases.py
test/test_prediction.py
test/test_pwmscan.py
test/test_rank.py
test/test_scanner.py
test/test_stats.py
test/test_tools.py
test/test_utils.py
test/data/background/genome.fa
test/data/background/genome.fa.fai
test/data/background/genome.fa.sizes
test/data/background/genome.gaps.bed
test/data/background/genome.size
test/data/background/test_gc1.bed
test/data/background/test_gc2.bed
test/data/background/test_gc3.bed
test/data/cli/Gm12878.CTCF.top200.fa
test/data/cli/cluster.pfm
test/data/cli/motifs.pfm
test/data/cli/test_motif.pfm
test/data/denovo/input.fa
test/data/denovo/input.fa.fai
test/data/denovo/random.fa
test/data/denovo/random.fa.fai
test/data/fasta/test.fa
test/data/fasta/test2.fa
test/data/fasta/test3.fa
test/data/filetype/bed.example1.txt
test/data/filetype/bed.example2.bed
test/data/filetype/bed.example3.txt
test/data/filetype/fasta.example1.txt
test/data/filetype/fasta.example2.fa
test/data/filetype/fasta.example3.fasta
test/data/filetype/narrowpeak.example1.narrowpeak
test/data/filetype/narrowpeak.example2.txt
test/data/filetype/narrowpeak.example3.np
test/data/filetype/unknown.example2.txt
test/data/genome_index/genes.bed
test/data/genome_index/genes.out
test/data/genome_index/test.bed
test/data/genome_index/track2fasta_result
test/data/genome_index/genome/genome.fa
test/data/genome_index/genome/genome.fa.fai
test/data/genome_index/genome/genome.fa.sizes
test/data/genome_index/genome/genome.gaps.bed
test/data/genomes/README.txt
test/data/genomes/hg38sample/hg38sample.fa
test/data/genomes/hg38sample/hg38sample.fa.fai
test/data/genomes/hg38sample/hg38sample.fa.sizes
test/data/genomes/hg38sample/hg38sample.gaps.bed
test/data/maelstrom/input.table.txt
test/data/maelstrom/motif.enrichment.png
test/data/maelstrom/motif.freq.txt
test/data/maelstrom/motif.frequency.png
test/data/maelstrom/motif.relevance.png
test/data/maelstrom/threshold.mm10.txt
test/data/moap/2clusters.motifs.count.txt
test/data/moap/2clusters.motifs.score.txt
test/data/moap/2clusters.txt
test/data/moap/clusters.txt
test/data/moap/motifs.count.txt
test/data/moap/motifs.score.txt
test/data/motifprogram/test.bg
test/data/motifprogram/test.fa
test/data/motifprogram/xxmotif.pwm
test/data/pwms/motifs.pwm
test/data/pwms/test.jaspar
test/data/pwmscan/10promoters.fa
test/data/pwmscan/TATA.pwm
test/data/pwmscan/enrichment.txt
test/data/pwmscan/promoters.fa
test/data/pwmscan/promoters.n5.fa
test/data/pwmscan/promoters_result.gff
test/data/pwmscan/random_sequences.fa
test/data/pwmscan/random_sequences.n5.fa
test/data/rank/rank_input.txt
test/data/rank/rank_output.txt
test/data/rank/ranked.txt
test/data/scan/scan_test_regions.bed
test/data/scan/scan_test_regions.fa
test/data/scan/genome/scan_test.fa
test/data/scanner/genome.fa
test/data/scanner/genome.fa.fai
test/data/scanner/genome.fa.sizes
test/data/scanner/genome.gaps.bed
test/data/scanner/motif.pwm
test/data/scanner/test.bed
test/data/scanner/test.fa
test/data/scanner/test.txt
test/data/stats/motifs.pwm
test/data/stats/p73.fa
test/data/stats/p73.scores.txt
test/data/stats/random.scores.txt
test/data/stats/random.w200.fa
test/data/stats/roc.txt
test/data/utils/test.bed
test/data/utils/test.fa
test/data/utils/test.narrowPeak
test/data/utils/test.txt