.coveragerc
.gitignore
.gitmodules
.pre-commit-config.yaml
.readthedocs.yml
AUTHORS.md
CHANGELOG.md
CONTRIBUTING.md
LICENSE.txt
README.md
pyproject.toml
setup.cfg
setup.py
tox.ini
.github/workflows/build-docs.yml
.github/workflows/publish-pypi.yml
.github/workflows/run-tests.yml
docs/Makefile
docs/authors.md
docs/changelog.md
docs/conf.py
docs/contributing.md
docs/index.md
docs/license.md
docs/readme.md
docs/requirements.txt
docs/_static/.gitignore
lib/CMakeLists.txt
lib/src/adt_quality_control.cpp
lib/src/aggregate_across_cells.cpp
lib/src/aggregate_across_genes.cpp
lib/src/block.h
lib/src/build_snn_graph.cpp
lib/src/center_size_factors.cpp
lib/src/choose_highly_variable_genes.cpp
lib/src/choose_pseudo_count.cpp
lib/src/cluster_graph.cpp
lib/src/cluster_kmeans.cpp
lib/src/combine_factors.cpp
lib/src/compute_clrm1_factors.cpp
lib/src/correct_mnn.cpp
lib/src/crispr_quality_control.cpp
lib/src/fit_variance_trend.cpp
lib/src/init.cpp
lib/src/model_gene_variances.cpp
lib/src/neighbors.h
lib/src/normalize_counts.cpp
lib/src/qc.h
lib/src/rna_quality_control.cpp
lib/src/run_pca.cpp
lib/src/run_tsne.cpp
lib/src/run_umap.cpp
lib/src/sanitize_size_factors.cpp
lib/src/scale_by_neighbors.cpp
lib/src/score_gene_set.cpp
lib/src/score_markers.cpp
lib/src/subsample_by_neighbors.cpp
lib/src/summarize_effects.cpp
lib/src/test_enrichment.cpp
lib/src/utils.h
src/scranpy/__init__.py
src/scranpy/_utils.py
src/scranpy/_utils_neighbors.py
src/scranpy/_utils_qc.py
src/scranpy/adt_quality_control.py
src/scranpy/aggregate_across_cells.py
src/scranpy/aggregate_across_genes.py
src/scranpy/analyze.py
src/scranpy/build_snn_graph.py
src/scranpy/center_size_factors.py
src/scranpy/choose_highly_variable_genes.py
src/scranpy/choose_pseudo_count.py
src/scranpy/cluster_graph.py
src/scranpy/cluster_kmeans.py
src/scranpy/combine_factors.py
src/scranpy/compute_clrm1_factors.py
src/scranpy/correct_mnn.py
src/scranpy/crispr_quality_control.py
src/scranpy/fit_variance_trend.py
src/scranpy/model_gene_variances.py
src/scranpy/normalize_counts.py
src/scranpy/rna_quality_control.py
src/scranpy/run_all_neighbor_steps.py
src/scranpy/run_pca.py
src/scranpy/run_tsne.py
src/scranpy/run_umap.py
src/scranpy/sanitize_size_factors.py
src/scranpy/scale_by_neighbors.py
src/scranpy/score_gene_set.py
src/scranpy/score_markers.py
src/scranpy/subsample_by_neighbors.py
src/scranpy/summarize_effects.py
src/scranpy/test_enrichment.py
src/scranpy.egg-info/PKG-INFO
src/scranpy.egg-info/SOURCES.txt
src/scranpy.egg-info/dependency_links.txt
src/scranpy.egg-info/not-zip-safe
src/scranpy.egg-info/requires.txt
src/scranpy.egg-info/top_level.txt
tests/conftest.py
tests/test_adt_quality_control.py
tests/test_aggregate_across_cells.py
tests/test_aggregate_across_genes.py
tests/test_analyze.py
tests/test_build_snn_graph.py
tests/test_center_size_factors.py
tests/test_choose_highly_variable_genes.py
tests/test_choose_pseudo_count.py
tests/test_cluster_graph.py
tests/test_cluster_kmeans.py
tests/test_combine_factors.py
tests/test_compute_clrm1_factors.py
tests/test_correct_mnn.py
tests/test_crispr_quality_control.py
tests/test_fit_variance_trend.py
tests/test_model_gene_variances.py
tests/test_normalize_counts.py
tests/test_rna_quality_control.py
tests/test_run_all_neighbor_steps.py
tests/test_run_pca.py
tests/test_run_tsne.py
tests/test_run_umap.py
tests/test_sanitize_size_factors.py
tests/test_scale_by_neighbors.py
tests/test_score_gene_set.py
tests/test_score_markers.py
tests/test_subsample_by_neighbors.py
tests/test_summarize_effects.py
tests/test_test_enrichment.py