.gitignore
Dockerfile
LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
.github/workflows/docker-ghcr.yml
.github/workflows/python-publish.yml
img/workflow.png
src/sniffcell/__init__.py
src/sniffcell/main.py
src/sniffcell/parse_args.py
src/sniffcell/sniffcell
src/sniffcell.egg-info/PKG-INFO
src/sniffcell.egg-info/SOURCES.txt
src/sniffcell.egg-info/dependency_links.txt
src/sniffcell.egg-info/entry_points.txt
src/sniffcell.egg-info/requires.txt
src/sniffcell.egg-info/top_level.txt
src/sniffcell/anno/__init__.py
src/sniffcell/anno/anno.py
src/sniffcell/anno/filter_bed_based_on_variants.py
src/sniffcell/anno/kmeans.py
src/sniffcell/anno/methyl_matrix.py
src/sniffcell/anno/variant_assignment.py
src/sniffcell/anno/vcf_to_df.py
src/sniffcell/archived_src/calc_methylation_diff_regions.py
src/sniffcell/archived_src/deconv.py
src/sniffcell/archived_src/deconv_em.py
src/sniffcell/archived_src/deconv_estimate.py
src/sniffcell/archived_src/dmr_region_finder.py
src/sniffcell/archived_src/figures.py
src/sniffcell/archived_src/get_base_modification_dictionary.py
src/sniffcell/archived_src/main.py
src/sniffcell/archived_src/parse_args.py
src/sniffcell/archived_src/process_ctdmr_regions.py
src/sniffcell/archived_src/region_deconv.py
src/sniffcell/archived_src/smoothing.py
src/sniffcell/archived_src/snp_post_filtering.py
src/sniffcell/archived_src/statistic_tests.py
src/sniffcell/archived_src/sv_annotation.py
src/sniffcell/archived_src/wgbs_uxm.py
src/sniffcell/deconv/__init__.py
src/sniffcell/deconv/deconv.py
src/sniffcell/dmsv/__init__.py
src/sniffcell/dmsv/dmsv.py
src/sniffcell/dmsv/statistical_test_around_sv.py
src/sniffcell/dmsv/sv_methylation.py
src/sniffcell/find/__init__.py
src/sniffcell/find/ctdmr.py
src/sniffcell/find/find.py
src/sniffcell/viz/__init__.py
src/sniffcell/viz/viz.py
tests/test_hierarchy_find_and_anno.py
tests/test_variant_assignment.py
tests/test_viz.py