CHANGELOG.md
CITATION.cff
COPYING
INSTALL
MANIFEST.in
README.md
compile_externals.py
setup.cfg
setup.py
versioneer.py
data/__init__.py
data/__pycache__/__init__.cpython-310.pyc
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.bed
data/examples/Gm12878.CTCF.top500.w200.fa
data/examples/MA0099.3.jaspar
data/examples/NRF1.bed
data/examples/TAp73alpha.bed
data/examples/TAp73alpha.fa
data/examples/example.pfm
data/examples/hg19.blood.most_variable.10k.txt
data/examples/hg19.blood.most_variable.1k.txt
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
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/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/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/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