.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.md
conftest.py
environment.yml
environment_minimal.yml
install_seqnado.sh
mkdocs.yml
pyproject.toml
seqnado_dev.yml
seqnado_logo.jpeg
setup.py
testing.yml
.github/dependabot.yml
.github/workflows/build_docs.yml
.github/workflows/publish_pypi_release.yml
.github/workflows/test_pipelines.yml
docs/cluster_config.md
docs/faq.md
docs/index.md
docs/installation.md
docs/pipeline.md
seqnado/__init__.py
seqnado/_version.py
seqnado/cli.py
seqnado/config.py
seqnado/design.py
seqnado/helpers.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/requires.txt
seqnado.egg-info/top_level.txt
seqnado/data/logo.txt
seqnado/workflow/snakefile_atac
seqnado/workflow/snakefile_build_index
seqnado/workflow/snakefile_chip
seqnado/workflow/snakefile_rna
seqnado/workflow/snakefile_snp
seqnado/workflow/config/config.yaml.jinja
seqnado/workflow/config/deseq2.qmd.jinja
seqnado/workflow/config/preset_genomes.json
seqnado/workflow/envs/environment.yml
seqnado/workflow/envs/profiles/profile_singularity/config.yaml
seqnado/workflow/envs/profiles/profile_slurm_singularity/config.yaml
seqnado/workflow/envs/profiles/profile_test/config.v8+.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/exogenous_norm.smk
seqnado/workflow/rules/fastq_screen.smk
seqnado/workflow/rules/fastq_trim.smk
seqnado/workflow/rules/heatmap.smk
seqnado/workflow/rules/hub.smk
seqnado/workflow/rules/motif.smk
seqnado/workflow/rules/peak_call_chip.smk
seqnado/workflow/rules/peak_call_grouped.smk
seqnado/workflow/rules/peak_call_other.smk
seqnado/workflow/rules/pileup_default.smk
seqnado/workflow/rules/pileup_grouped.smk
seqnado/workflow/rules/pileup_norm.smk
seqnado/workflow/rules/qc.smk
seqnado/workflow/rules/variant.smk
seqnado/workflow/scripts/calculate_scaling_factors.R
seqnado/workflow/scripts/calculate_spikein_norm_factors.py
seqnado/workflow/scripts/calculate_spikein_norm_factors_rna.R
seqnado/workflow/scripts/calculate_spikein_norm_orlando.py
seqnado/workflow/scripts/create_hub.py
seqnado/workflow/scripts/get_salmon_counts.py
seqnado/workflow/scripts/remove_blacklist.py
seqnado/workflow/scripts/remove_duplicates.py
seqnado/workflow/scripts/shift_alignments.py
tests/test_pipelines.py