.gitignore
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
.github/workflows/python-publish.yml
docs/README.md
docs/envs/map3C_rna.yaml
docs/envs/map3C_snakemake.yml
docs/envs/map3C_tools.yml
docs/envs/map3C_utils.yml
docs/envs/preprocess/map3C_preprocess_cutadapt.yml
docs/envs/preprocess/map3C_preprocess_hires.yml
docs/envs/preprocess/map3C_preprocess_meta.yml
docs/instructions/HiRES/README.md
docs/instructions/HiRES/scripts/A02a_prepare_mapping.sh
docs/instructions/HiRES/scripts/A02b_run_mapping.sh
docs/instructions/HiRES/txt/mapping_config_HiRES.yml
docs/instructions/HiRES/txt/mapping_info.txt
docs/instructions/LiMCA/README.md
docs/instructions/LiMCA/scripts/A02a_prepare_mapping.sh
docs/instructions/LiMCA/scripts/A02b_run_mapping.sh
docs/instructions/LiMCA/txt/mapping_config_LiMCA.yml
docs/instructions/LiMCA/txt/mapping_info.txt
docs/instructions/snm3C-seq/README.md
docs/instructions/snm3C-seq/scripts/A01a_prepare_demultiplex.sh
docs/instructions/snm3C-seq/scripts/A01b_run_demultiplex.sh
docs/instructions/snm3C-seq/scripts/A02a_prepare_mapping.sh
docs/instructions/snm3C-seq/scripts/A02b_run_mapping.sh
docs/instructions/snm3C-seq/txt/demultiplex_config_snm3C.yml
docs/instructions/snm3C-seq/txt/mapping_config_snm3C.yml
docs/instructions/snm3C-seq/txt/mapping_info.txt
docs/instructions/snm3C-seq/txt/plate_info.txt
docs/instructions/snm3C-seq/txt/random_index_v2.multiplex.fa
docs/instructions/snmCT-seq/README.md
docs/instructions/snmCT-seq/scripts/A01a_prepare_demultiplex.sh
docs/instructions/snmCT-seq/scripts/A01b_run_demultiplex.sh
docs/instructions/snmCT-seq/scripts/A02a_prepare_mapping.sh
docs/instructions/snmCT-seq/scripts/A02b_run_mapping.sh
docs/instructions/snmCT-seq/txt/demultiplex_config_snmCT.yml
docs/instructions/snmCT-seq/txt/mapping_config_snmCT.yml
docs/instructions/snmCT-seq/txt/mapping_info.txt
docs/instructions/snmCT-seq/txt/plate_info.txt
docs/instructions/snmCT-seq/txt/random_index_v2.multiplex.fa
map3C/__init__.py
map3C/__main__.py
map3C/_version.py
map3C.egg-info/PKG-INFO
map3C.egg-info/SOURCES.txt
map3C.egg-info/dependency_links.txt
map3C.egg-info/entry_points.txt
map3C.egg-info/top_level.txt
map3C/demultiplex/__init__.py
map3C/demultiplex/demultiplex.py
map3C/demultiplex/snakemake/GAGE-seq/demultiplex_BC1.smk
map3C/demultiplex/snakemake/GAGE-seq/demultiplex_BC2.smk
map3C/demultiplex/snakemake/snm3Cseq/demultiplex.smk
map3C/mapping/__init__.py
map3C/mapping/allc.py
map3C/mapping/call_contacts.py
map3C/mapping/compute_restriction_sites.py
map3C/mapping/contam_filter.py
map3C/mapping/cut_analysis.py
map3C/mapping/mapping.py
map3C/mapping/mask.py
map3C/mapping/pairs_generator.py
map3C/mapping/pairtools.py
map3C/mapping/phase.py
map3C/mapping/utils.py
map3C/mapping/snakemake/m3C/mapping.smk
map3C/mapping/snakemake/m3C/rules/align.smk
map3C/mapping/snakemake/m3C/rules/align_bisulfite.smk
map3C/mapping/snakemake/m3C/rules/align_dna.smk
map3C/mapping/snakemake/m3C/rules/allc.smk
map3C/mapping/snakemake/m3C/rules/contacts.smk
map3C/mapping/snakemake/m3C/rules/coord_sort_bam.smk
map3C/mapping/snakemake/m3C/rules/dedup_contacts.smk
map3C/mapping/snakemake/m3C/rules/lowcov_contacts.smk
map3C/mapping/snakemake/m3C/rules/mask.smk
map3C/mapping/snakemake/m3C/rules/merge_sort.smk
map3C/mapping/snakemake/m3C/rules/mkdup.smk
map3C/mapping/snakemake/m3C/rules/mkdup_bisulfite.smk
map3C/mapping/snakemake/m3C/rules/preprocess.smk
map3C/mapping/snakemake/m3C/rules/read_analysis.smk
map3C/mapping/snakemake/m3C/rules/reformat.smk
map3C/mapping/snakemake/m3C/rules/sort_contacts.smk
map3C/mapping/snakemake/m3C/rules/stats.smk
map3C/mapping/snakemake/m3C/rules/trim/trim_cutadapt_pe.smk
map3C/mapping/snakemake/m3C/rules/trim/trim_hires.smk
map3C/mapping/snakemake/m3C/rules/trim/trim_meta.smk
map3C/mapping/snakemake/mCT/mapping.smk
map3C/mapping/snakemake/mCT/rules/align.smk
map3C/mapping/snakemake/mCT/rules/align_biscuit.smk
map3C/mapping/snakemake/mCT/rules/align_star.smk
map3C/mapping/snakemake/mCT/rules/postprocess.smk
map3C/mapping/snakemake/mCT/rules/postprocess_dna.smk
map3C/mapping/snakemake/mCT/rules/postprocess_rna.smk
map3C/mapping/snakemake/mCT/rules/preprocess.smk
map3C/mapping/snakemake/mCT/rules/stats.smk
map3C/mapping/snakemake/mCT/rules/trim/trim_cutadapt_pe.smk