.bumpversion.cfg
.dockerignore
.pre-commit-config.yaml
.readthedocs.yaml
LICENSE
MANIFEST.in
README.rst
pyproject.toml
setup.cfg
setup.py
docs/Makefile
docs/conf.py
docs/index.rst
docs/make.bat
docs/robots.txt
docs/zreferences.bib
docs/zreferences.rst
docs/tutorials/additional_functions.ipynb
docs/tutorials/comparing_imodulons.ipynb
docs/tutorials/creating_the_gene_table.ipynb
docs/tutorials/gene_enrichment_analysis.ipynb
docs/tutorials/imodulon_thresholds.ipynb
docs/tutorials/inferring_imodulon_activities_for_new_data.ipynb
docs/tutorials/introduction_to_the_ica_data_object.ipynb
docs/tutorials/plotting_functions.ipynb
docs/tutorials/searching_for_motifs.ipynb
docs/tutorials/tmp/.gitignore
docs/tutorials/tmp/ArgR.fasta
docs/tutorials/tmp/ecoli_data.json
docs/tutorials/tmp/ArgR/logo1.eps
docs/tutorials/tmp/ArgR/logo1.png
docs/tutorials/tmp/ArgR/logo2.eps
docs/tutorials/tmp/ArgR/logo2.png
docs/tutorials/tmp/ArgR/logo_rc1.eps
docs/tutorials/tmp/ArgR/logo_rc1.png
docs/tutorials/tmp/ArgR/logo_rc2.eps
docs/tutorials/tmp/ArgR/logo_rc2.png
docs/tutorials/tmp/ArgR/meme.html
docs/tutorials/tmp/ArgR/meme.txt
docs/tutorials/tmp/ArgR/meme.xml
docs/tutorials/tmp/ArgR/tomtom/align_TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR_0_+MX000116.png
docs/tutorials/tmp/ArgR/tomtom/align_TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR_0_-MX000043.png
docs/tutorials/tmp/ArgR/tomtom/align_TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR_1_-argR.png
docs/tutorials/tmp/ArgR/tomtom/align_TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR_1_-argR2.png
docs/tutorials/tmp/ArgR/tomtom/align_TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR_2_+MX000116.png
docs/tutorials/tmp/ArgR/tomtom/align_TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR_2_-MX000043.png
docs/tutorials/tmp/ArgR/tomtom/align_TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR_4_-ArgR_26-5.png
docs/tutorials/tmp/ArgR/tomtom/tomtom.html
docs/tutorials/tmp/ArgR/tomtom/tomtom.tsv
docs/tutorials/tmp/ArgR/tomtom/tomtom.xml
notebooks/Tutorial.ipynb
notebooks/iModulonDB_setup.ipynb
notebooks/iModulon_characterization.ipynb
src/pymodulon/__init__.py
src/pymodulon/compare.py
src/pymodulon/core.py
src/pymodulon/enrichment.py
src/pymodulon/example_data.py
src/pymodulon/gene_util.py
src/pymodulon/imodulondb.py
src/pymodulon/io.py
src/pymodulon/motif.py
src/pymodulon/plotting.py
src/pymodulon/util.py
src/pymodulon.egg-info/PKG-INFO
src/pymodulon.egg-info/SOURCES.txt
src/pymodulon.egg-info/dependency_links.txt
src/pymodulon.egg-info/requires.txt
src/pymodulon.egg-info/top_level.txt
src/pymodulon/data/bbh/example_bbh.csv
src/pymodulon/data/ecoli/A.csv
src/pymodulon/data/ecoli/GO_example_annotations.txt
src/pymodulon/data/ecoli/M.csv
src/pymodulon/data/ecoli/X.csv
src/pymodulon/data/ecoli/biocyc_operon_annotations.txt
src/pymodulon/data/ecoli/eggNOG_annotations.txt
src/pymodulon/data/ecoli/example_tpm.csv
src/pymodulon/data/ecoli/gene_table.csv
src/pymodulon/data/ecoli/genome.fasta
src/pymodulon/data/ecoli/genome.gff3
src/pymodulon/data/ecoli/imodulon_table.csv
src/pymodulon/data/ecoli/log_tpm.csv
src/pymodulon/data/ecoli/sample_table.csv
src/pymodulon/data/ecoli/trn.csv
src/pymodulon/data/meme/SwissRegulon_e_coli.meme
src/pymodulon/data/meme/collectf.meme
src/pymodulon/data/meme/dpinteract.meme
src/pymodulon/data/meme/prodoric.meme
src/pymodulon/data/meme/regtransbase.meme
src/pymodulon/data/objects/bsub_data.json.gz
src/pymodulon/data/objects/ecoli_data.json.gz
src/pymodulon/data/objects/staph_data.json.gz
tests/__init__.py
tests/conftest.py
tests/test_compare.py
tests/test_core.py
tests/test_enrichment.py
tests/test_io.py
tests/data/genome.gb
tests/data/proteins.faa
tests/data/truncated_proteins.faa