.gitignore
CLAUDE.md
Dockerfile
LICENSE
README.md
mkdocs.yml
pyproject.toml
setup.py
uv.lock
.github/workflows/build-container.yml
.github/workflows/deploy-docs.yml
.github/workflows/pypi.yml
.github/workflows/python-tests.yml
docs/basic_usage.md
docs/cli.md
docs/examples.md
docs/faq.md
docs/index.md
docs/installation.md
docs/quick_start.md
docs/troubleshooting.md
docs/api/bamstore.md
docs/api/methylstore.md
docs/api/quantnado.md
docs/api/quantnadodataset.md
docs/api/variantstore.md
docs/assets/images/logo.png
docs/cli/call_peaks.md
docs/cli/combine_dataset.md
docs/cli/create_dataset.md
docs/cli/index.md
docs/example/example_dataset.ipynb
docs/example/example_dataset.sh
profiling/profiling.py
quantnado/__init__.py
quantnado/_version.py
quantnado/api.py
quantnado/cli.py
quantnado/utils.py
quantnado.egg-info/PKG-INFO
quantnado.egg-info/SOURCES.txt
quantnado.egg-info/dependency_links.txt
quantnado.egg-info/entry_points.txt
quantnado.egg-info/requires.txt
quantnado.egg-info/top_level.txt
quantnado/analysis/__init__.py
quantnado/analysis/core.py
quantnado/analysis/counts.py
quantnado/analysis/features.py
quantnado/analysis/normalise.py
quantnado/analysis/pca.py
quantnado/analysis/peaks.py
quantnado/analysis/plot.py
quantnado/analysis/ranges.py
quantnado/analysis/reduce.py
quantnado/dataset/__init__.py
quantnado/dataset/combine_multiomics.py
quantnado/dataset/core.py
quantnado/dataset/metadata.py
quantnado/dataset/store_bam.py
quantnado/dataset/store_coverage.py
quantnado/dataset/store_methyl.py
quantnado/dataset/store_multiomics.py
quantnado/dataset/store_variants.py
quantnado/dataset/utils.py
quantnado/peak_calling/__init__.py
quantnado/peak_calling/_device.py
quantnado/peak_calling/call_lanceotron_peaks.py
quantnado/peak_calling/call_quantile_peaks.py
quantnado/peak_calling/call_seacr_peaks.py
quantnado/peak_calling/static/lanceotron/deep_scaler_mean.npy
quantnado/peak_calling/static/lanceotron/deep_scaler_scale.npy
quantnado/peak_calling/static/lanceotron/lanceotron_v5_03.pt
quantnado/peak_calling/static/lanceotron/wide_scaler_mean.npy
quantnado/peak_calling/static/lanceotron/wide_scaler_scale.npy
scripts/setup_lanceotron_weights.py
tests/conftest.py
tests/cli/test_cli.py
tests/data/MV411-CAT_MLL-N-1_subsample.bam
tests/data/MV411-CAT_MLL-N-1_subsample.bam.bai
tests/data/OCI-AML3-control-1-1-A_subsample.bam
tests/data/OCI-AML3-control-1-1-A_subsample.bam.bai
tests/data/test.vcf.gz
tests/data/seacr/CT-SEM_H3K27ac_chr7_9_13.bdg
tests/data/seacr/CT-SEM_MLL_chr7_9_13.bdg
tests/data/seacr/CTCF_DE_chr1_100Mb.bedgraph.txt
tests/data/seacr/CTCF_DE_chr1_100Mb.relaxed.bed.txt
tests/data/seacr/CTCF_DE_chr1_100Mb.stringent.bed.txt
tests/data/seacr/IgG_DE_chr1_100Mb.bedgraph.txt
tests/data/seacr/Test_README.md
tests/integration/__init__.py
tests/integration/test_bam_store.py
tests/integration/test_bam_store_real.py
tests/integration/test_peak_calling.py
tests/integration/test_quantnado_dataset.py
tests/unit/__init__.py
tests/unit/conftest.py
tests/unit/test_device.py
tests/unit/test_enums.py
tests/unit/test_features.py
tests/unit/test_info.py
tests/unit/test_metadata.py
tests/unit/test_normalise.py
tests/unit/test_pca.py
tests/unit/test_peak_api.py
tests/unit/test_plot.py
tests/unit/test_ranges.py
tests/unit/test_rna_stranding.py
tests/unit/test_subset_metadata.py