.gitignore
.travis.yml
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
cemba_data/__init__.py
cemba_data/__main__.py
cemba_data/_yap_internal_cli_.py
cemba_data/qsub.py
cemba_data/sbatch.py
cemba_data/utilities.py
cemba_data.egg-info/PKG-INFO
cemba_data.egg-info/SOURCES.txt
cemba_data.egg-info/dependency_links.txt
cemba_data.egg-info/entry_points.txt
cemba_data.egg-info/requires.txt
cemba_data.egg-info/top_level.txt
cemba_data/bulk/__init__.py
cemba_data/bulk/mc_bulk.py
cemba_data/bulk/Snakefile_template/__init__.py
cemba_data/bulk/Snakefile_template/mc_bulk.Snakefile
cemba_data/demultiplex/__init__.py
cemba_data/demultiplex/demultiplex.py
cemba_data/demultiplex/fastq_dataframe.py
cemba_data/demultiplex/plateinfo_and_samplesheet.py
cemba_data/dmr/__init__.py
cemba_data/dmr/dmrseq/DMRseq.ipynb
cemba_data/dmr/dmrseq/__init__.py
cemba_data/dmr/dss/DSS.MultiGroup.SingleRegionDML.ipynb
cemba_data/dmr/dss/DSS.TwoGroup.SingleRegionDML.ipynb
cemba_data/dmr/dss/MultiGroup.py
cemba_data/dmr/dss/TwoGroup.py
cemba_data/dmr/dss/__init__.py
cemba_data/files/V1_i7_i5_index.tsv
cemba_data/files/V2_i7_i5_index.tsv
cemba_data/files/__init__.py
cemba_data/files/plate_info_template_v1.txt
cemba_data/files/plate_info_template_v2.txt
cemba_data/files/random_index_v1.fa
cemba_data/files/sample_sheet_header.txt
cemba_data/files/sbatch_template.txt
cemba_data/files/default_config/__init__.py
cemba_data/files/default_config/mapping_config_m3c.ini
cemba_data/files/default_config/mapping_config_mc.ini
cemba_data/files/default_config/mapping_config_mct-nome.ini
cemba_data/files/default_config/mapping_config_mct.ini
cemba_data/files/default_config/mapping_config_nome.ini
cemba_data/files/mapping_summary_template/__init__.py
cemba_data/files/mapping_summary_template/m3c_template.ipynb
cemba_data/files/mapping_summary_template/mc_template.ipynb
cemba_data/files/mapping_summary_template/mct_template.ipynb
cemba_data/files/random_index_v2/__init__.py
cemba_data/files/random_index_v2/random_index_v2.fa
cemba_data/files/random_index_v2/random_index_v2.multiplex_group_1.fa
cemba_data/files/random_index_v2/random_index_v2.multiplex_group_2.fa
cemba_data/files/random_index_v2/random_index_v2.multiplex_group_3.fa
cemba_data/files/random_index_v2/random_index_v2.multiplex_group_4.fa
cemba_data/files/random_index_v2/random_index_v2.multiplex_group_5.fa
cemba_data/files/random_index_v2/random_index_v2.multiplex_group_6.fa
cemba_data/mapping/__init__.py
cemba_data/mapping/config.py
cemba_data/mapping/test_environment.py
cemba_data/mapping/Snakefile_template/__init__.py
cemba_data/mapping/Snakefile_template/m3c.Snakefile
cemba_data/mapping/Snakefile_template/mc.Snakefile
cemba_data/mapping/Snakefile_template/mct.Snakefile
cemba_data/mapping/m3c/__init__.py
cemba_data/mapping/mct/__init__.py
cemba_data/mapping/mct/mct_bismark_bam_filter.py
cemba_data/mapping/mct/mct_star_bam_filter.py
cemba_data/mapping/pipelines/__init__.py
cemba_data/mapping/pipelines/m3c.py
cemba_data/mapping/pipelines/mc.py
cemba_data/mapping/pipelines/mct.py
cemba_data/mapping/stats/__init__.py
cemba_data/mapping/stats/m3c.py
cemba_data/mapping/stats/mc.py
cemba_data/mapping/stats/mct.py
cemba_data/mapping/stats/plate_info.py
cemba_data/mapping/stats/plot.py
cemba_data/mapping/stats/utilities.py
cemba_data/snm3C/__init__.py
cemba_data/snm3C/prepare_dataset.py
cemba_data/snm3C/prepare_impute.py
doc/Makefile
doc/Mapping.ipynb
doc/MappingSummary.ipynb
doc/PipelineInput.ipynb
doc/PlateInfoAndSampleSheet.ipynb
doc/TODO_GenerateMCDS.ipynb
doc/TODO_overview.ipynb
doc/TechBasic.ipynb
doc/conf.py
doc/demultiplex.ipynb
doc/index.rst
doc/installation.ipynb
doc/make.bat
doc/archive/MakeFastqDataframe.ipynb
doc/files/MappingPipeline.png
doc/files/molecularsteps.png
doc/files/primerstructure.png
doc/files/v1barcode.png
doc/files/v2barcode.png