.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.md
environment.yml
pyproject.toml
setup.cfg
setup.py
testing.yml
.github/workflows/test_pipelines.yml
config/config_atac.yml
config/config_chip.yml
config/config_rna.yml
seqnado/__init__.py
seqnado/cli.py
seqnado/utils.py
seqnado/utils_chipseq.py
seqnado.egg-info/PKG-INFO
seqnado.egg-info/SOURCES.txt
seqnado.egg-info/dependency_links.txt
seqnado.egg-info/entry_points.txt
seqnado.egg-info/not-zip-safe
seqnado.egg-info/requires.txt
seqnado.egg-info/top_level.txt
seqnado/data/cookiecutter_config/config_atac/hooks/generate_samplesheet.py
seqnado/data/cookiecutter_config/config_atac/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_atac.yml
seqnado/data/cookiecutter_config/config_chip/hooks/generate_samplesheet.py
seqnado/data/cookiecutter_config/config_chip/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_chip.yml
seqnado/data/cookiecutter_config/config_rna/hooks/generate_samplesheet.py
seqnado/data/cookiecutter_config/config_rna/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_rna.yml
seqnado/data/cookiecutter_config/config_snp/hooks/generate_samplesheet.py
seqnado/data/cookiecutter_config/config_snp/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_snp.yml
seqnado/data/profiles/profile_drmaa_singularity/config.yaml
seqnado/data/profiles/profile_singularity/config.yaml
seqnado/workflow/snakefile_atac
seqnado/workflow/snakefile_build_index
seqnado/workflow/snakefile_chip
seqnado/workflow/snakefile_rna
seqnado/workflow/snakefile_snp
seqnado/workflow/envs/environment.yml
seqnado/workflow/envs/profiles/profile_drmaa_singularity/config.yaml
seqnado/workflow/envs/profiles/profile_singularity/config.yaml
seqnado/workflow/rules/align.smk
seqnado/workflow/rules/align_rna.smk
seqnado/workflow/rules/alignment_counts.smk
seqnado/workflow/rules/alignment_post_processing.smk
seqnado/workflow/rules/custom_genome.smk
seqnado/workflow/rules/deseq2_rna.smk
seqnado/workflow/rules/fastq_trim.smk
seqnado/workflow/rules/heatmap.smk
seqnado/workflow/rules/hub.smk
seqnado/workflow/rules/hub_rna.smk
seqnado/workflow/rules/peak_call.smk
seqnado/workflow/rules/pileup.smk
seqnado/workflow/rules/pileup_rna.smk
seqnado/workflow/rules/qc.smk
seqnado/workflow/rules/variant.smk
seqnado/workflow/scripts/create_hub_genomics.py
seqnado/workflow/scripts/create_hub_transcriptomics.py
seqnado/workflow/scripts/remove_blacklist.py
seqnado/workflow/scripts/remove_duplicates.py
seqnado/workflow/scripts/shift_alignments.py
tests/test_atac.py
tests/test_chip.py
tests/test_rna.py
tests/data/config/config_atac.yml
tests/data/config/config_chip.yml
tests/data/config/config_rna.yml
tests/old/old_test_atac.py
tests/old/old_test_chip_paired.py
tests/old/old_test_chip_single.py
tests/old/old_test_rna.py
tests/old/old_test_smk_chip.py