.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
CHANGELOG.md
LICENSE
README.md
pixi.lock
pyproject.toml
.github/dependabot.yml
.github/workflows/pixi.yml
.github/workflows/pypi.yml
.github/workflows/release-please.yml
docs/conf.py
docs/index.rst
docs/content/example.rst
docs/content/installation.rst
docs/content/usage.rst
src/ATACofthesnake.egg-info/PKG-INFO
src/ATACofthesnake.egg-info/SOURCES.txt
src/ATACofthesnake.egg-info/dependency_links.txt
src/ATACofthesnake.egg-info/entry_points.txt
src/ATACofthesnake.egg-info/requires.txt
src/ATACofthesnake.egg-info/top_level.txt
src/aos/__init__.py
src/aos/atac.py
src/aos/example.py
src/aos/gp_custom_kernels.py
src/aos/gp_fitter.py
src/aos/helper.py
src/aos/logger.py
src/aos/preflight.py
src/aos/workflow.smk
src/aos/rules/1_peaks.smk
src/aos/rules/1_qc.smk
src/aos/rules/2_gp_de.smk
src/aos/rules/2_lrt_de.smk
src/aos/rules/2_twogroup_de.smk
src/aos/rules/3_collate_sigresults.smk
src/aos/rules/3_motifs.smk
src/aos/rules/3_tobias.smk
src/aos/rules/envs/deeptools.yml
src/aos/rules/envs/gimmemotifs.yml
src/aos/rules/envs/gp.yml
src/aos/rules/envs/meme.yml
src/aos/rules/envs/seqtools.yml
src/aos/rules/envs/tobias.yml
src/aos/rules/scripts/edger_lrt.R
src/aos/rules/scripts/edger_twogroup.R
src/aos/rules/scripts/gp.py
src/aos/rules/scripts/gp_interaction.py
src/aos/rules/scripts/gp_postprocess.py
src/aos/rules/scripts/plot_ame.py
src/aos/rules/scripts/scalefactors.R
src/aos/tests/conftest.py
src/aos/tests/test_preflight.py