├── .github └── workflows │ └── publish.yaml ├── .gitignore ├── .travis.yml ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── cemba_data ├── __init__.py ├── __main__.py ├── _yap_internal_cli_.py ├── bulk │ ├── Snakefile_template │ │ ├── __init__.py │ │ └── mc_bulk.Snakefile │ ├── __init__.py │ ├── atac_bulk.py │ ├── mc_bulk.py │ ├── mc_bulk_multigroup │ │ ├── __init__.py │ │ ├── mc_bulk_multigroup.py │ │ └── mc_bulk_multigroup_template.py │ └── mct_bulk.py ├── demultiplex │ ├── __init__.py │ ├── demultiplex.py │ ├── fastq_dataframe.py │ └── plateinfo_and_samplesheet.py ├── dmr │ ├── __init__.py │ ├── dmrseq │ │ ├── DMRseq.ipynb │ │ └── __init__.py │ └── dss │ │ ├── DSS.MultiGroup.SingleRegionDML.ipynb │ │ ├── DSS.TwoGroup.SingleRegionDML.ipynb │ │ ├── MultiGroup.py │ │ ├── TwoGroup.py │ │ └── __init__.py ├── files │ ├── V1_i7_i5_index.tsv │ ├── V2_i7_i5_index.tsv │ ├── __init__.py │ ├── default_config │ │ ├── __init__.py │ │ ├── mapping_config_4m.ini │ │ ├── mapping_config_m3c.ini │ │ ├── mapping_config_mc.ini │ │ ├── mapping_config_mct-nome.ini │ │ ├── mapping_config_mct.ini │ │ └── mapping_config_nome.ini │ ├── mapping_summary_template │ │ ├── 4m_template.ipynb │ │ ├── __init__.py │ │ ├── m3c_template.ipynb │ │ ├── mc_template.ipynb │ │ └── mct_template.ipynb │ ├── plate_info_template_v1.txt │ ├── plate_info_template_v2.txt │ ├── random_index_v1.fa │ ├── random_index_v2 │ │ ├── __init__.py │ │ ├── random_index_v2.fa │ │ ├── random_index_v2.multiplex_group_1.fa │ │ ├── random_index_v2.multiplex_group_2.fa │ │ ├── random_index_v2.multiplex_group_3.fa │ │ ├── random_index_v2.multiplex_group_4.fa │ │ ├── random_index_v2.multiplex_group_5.fa │ │ └── random_index_v2.multiplex_group_6.fa │ ├── sample_sheet_header.txt │ ├── sbatch_template_schicluster.txt │ └── sbatch_template_yap.txt ├── hisat3n │ ├── __init__.py │ ├── cli.py │ ├── config │ │ ├── __init__.py │ │ ├── gcp.md │ │ ├── hisat-3n-build.sh │ │ ├── hisat3n_mapping_env.yaml │ │ └── vm_init.sh │ ├── hisat3n_general.py │ ├── hisat3n_m3c.py │ ├── hisat3n_mct.py │ ├── snakefile │ │ ├── __init__.py │ │ ├── m3c.smk │ │ ├── mc-multi.smk │ │ ├── mc-multi_sort_input.smk │ │ ├── mc.smk │ │ ├── mct-multi.smk │ │ └── mct.smk │ ├── stats_col_names.py │ ├── stats_parser.py │ ├── summary.py │ └── utilities.py ├── mapping │ ├── Snakefile_template │ │ ├── 4m.Snakefile │ │ ├── __init__.py │ │ ├── m3c.Snakefile │ │ ├── mc.Snakefile │ │ └── mct.Snakefile │ ├── __init__.py │ ├── config.py │ ├── m3c │ │ └── __init__.py │ ├── mct │ │ ├── __init__.py │ │ ├── mct_bismark_bam_filter.py │ │ └── mct_star_bam_filter.py │ ├── pipelines │ │ ├── _4m.py │ │ ├── __init__.py │ │ ├── m3c.py │ │ ├── mc.py │ │ └── mct.py │ ├── stats │ │ ├── _4m.py │ │ ├── __init__.py │ │ ├── m3c.py │ │ ├── mc.py │ │ ├── mct.py │ │ ├── plate_info.py │ │ ├── plot.py │ │ └── utilities.py │ └── test_environment.py ├── qsub.py ├── sbatch.py ├── snm3C │ ├── __init__.py │ ├── prepare_dataset.py │ └── prepare_impute.py └── 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