.gitignore
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CHANGES.md
Dockerfile
LICENSE
README.md
peakqc_env.yml
pyproject.toml
.gitlab/new_release_template.md
dist/peakqc-0.1.3-py3-none-any.whl
dist/peakqc-0.1.3.tar.gz
dist/peakqc-0.1.4-py3-none-any.whl
dist/peakqc-0.1.4.tar.gz
docs/Makefile
docs/make.bat
docs/source/build_api.py
docs/source/conf.py
docs/source/index.rst
docs/source/installation.rst
docs/source/quickstart.rst
docs/source/API/index.rst
docs/source/_static/logo.png
figures/PEAKQC_workflow.drawio
figures/PEAKQC_workflow.drawio.png
figures/aspects_atac_qc.png
paper/PP_reference.ipynb
paper/example_notebook.ipynb
paper/preprocessing-ontology.ipynb
paper/benchmark/Benchmark.ipynb
paper/benchmark/distance_score_scatter.png
paper/benchmark/plotting_scores.ipynb
paper/fld-metrics/threshold_impacts.ipynb
paper/metric-specifity/filter-specifity.ipynb
paper/preprocessing/notebooks/pipeline.ipynb
paper/preprocessing/package/README.adoc
paper/preprocessing/package/setup.py
paper/preprocessing/package/fastq2anndata/converter.py
paper/preprocessing/package/fastq2anndata/fastq2anndata.py
paper/preprocessing/package/fastq2anndata/fastqToAnndata.sh
paper/preprocessing/package/fastq2anndata/run_macs.sh
paper/preprocessing/package/fastq2anndata/snapAddPMAT.sh
paper/rare_cells_cluster/.pybiomart.sqlite
paper/rare_cells_cluster/03_normalization_batch_correction.ipynb
paper/rare_cells_cluster/04_clustering.ipynb
paper/rare_cells_cluster/config.yaml
paper/rare_cells_cluster/group_markers.ipynb
paper/rare_cells_cluster/figures/umap-random-ontology-peakqc.png
scripts/collect_changes.py
src/PEAKQC.egg-info/PKG-INFO
src/PEAKQC.egg-info/SOURCES.txt
src/PEAKQC.egg-info/dependency_links.txt
src/PEAKQC.egg-info/requires.txt
src/PEAKQC.egg-info/top_level.txt
src/peakqc/__init__.py
src/peakqc/_version.py
src/peakqc/fld_scoring.py
src/peakqc/general.py
src/peakqc/insertsizes.py
tests/__init__.py
tests/test_fld_scoring.py
tests/test_insertsizes.py
tests/data/fld_scoring_related/count_table_heart_lv.csv
tests/data/fld_scoring_related/nucleosomal_score.csv
tests/data/fld_scoring_related/subsetted_adata.h5ad
tests/data/insertsizes_related/200_lines_atac_pbmc_5k_nextgem_fragments.tsv.gz
tests/data/insertsizes_related/barcodes.txt
tests/data/insertsizes_related/example_chunk.csv
tests/data/insertsizes_related/fragments_heart_left_ventricle_head_100k.bed
tests/data/insertsizes_related/heart_left_ventricle_1mio.bam
tests/data/insertsizes_related/heart_left_ventricle_1mio.bam.bai