CHANGELOG.md
COPYING
INSTALL
MANIFEST.in
README.md
compile_externals.py
setup.cfg
setup.py
versioneer.py
data/__init__.py
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/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/sortable/sortable-theme-slick.css
data/templates/sortable/sortable.min.js
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/motif.py
gimmemotifs/plot.py
gimmemotifs/prediction.py
gimmemotifs/rank.py
gimmemotifs/report.py
gimmemotifs/rocmetrics.py
gimmemotifs/scanner.py
gimmemotifs/shutils.py
gimmemotifs/stats.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/motifs.py
gimmemotifs/commands/pfmscan.py
gimmemotifs/commands/prediction.py
gimmemotifs/commands/threshold.py
gimmemotifs/db/__init__.py
gimmemotifs/included_tools/__init__.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/gimme
src/COPYING
src/README
src/AMD/AMD.bin
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.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_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.sizes
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/random.fa
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/genomes/README.txt
test/data/genomes/hg38sample/hg38sample.fa
test/data/genomes/hg38sample/hg38sample.fa.sizes
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/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