.gitignore
.readthedocs.yaml
LICENSE
PROMOTION_PLAN.md
README.md
pyproject.toml
.github/workflows/ci.yml
.github/workflows/publish.yml
conda-recipe/meta.yaml
docs/api.rst
docs/cli.rst
docs/conf.py
docs/index.rst
docs/installation.rst
docs/quickstart.rst
docs/vignettes/index.rst
examples/basic_config.yaml
examples/cross_platform_config.yaml
examples/demo.ipynb
examples/sample_rcc/Sample_1_Lung.RCC
examples/sample_rcc/Sample_2_Lung.RCC
examples/sample_rcc/Sample_3_Lung.RCC
examples/vignettes/GSE117751_autoimmune_retinopathy.ipynb
examples/vignettes/GSE140901_hcc_immunotherapy.ipynb
examples/vignettes/GSE268012_ifn_macrophages.ipynb
examples/vignettes/GSE275334_long_covid.ipynb
examples/vignettes/GSE74821_breast_cancer_pam50.ipynb
joss/paper.bib
joss/paper.md
scverse-submission/meta.yaml
src/ncountr/__init__.py
src/ncountr/__main__.py
src/ncountr/cli.py
src/ncountr/config.py
src/ncountr/datasets.py
src/ncountr/experiment.py
src/ncountr.egg-info/PKG-INFO
src/ncountr.egg-info/SOURCES.txt
src/ncountr.egg-info/dependency_links.txt
src/ncountr.egg-info/entry_points.txt
src/ncountr.egg-info/requires.txt
src/ncountr.egg-info/top_level.txt
src/ncountr/core/__init__.py
src/ncountr/core/de.py
src/ncountr/core/normalize.py
src/ncountr/core/pathway.py
src/ncountr/core/qc.py
src/ncountr/crossplatform/__init__.py
src/ncountr/crossplatform/composition.py
src/ncountr/crossplatform/concordance.py
src/ncountr/crossplatform/correlation.py
src/ncountr/crossplatform/crossreactivity.py
src/ncountr/crossplatform/loaders.py
src/ncountr/io/__init__.py
src/ncountr/io/export.py
src/ncountr/io/geo.py
src/ncountr/io/rcc.py
src/ncountr/plotting/__init__.py
src/ncountr/plotting/correlation_plots.py
src/ncountr/plotting/de_plots.py
src/ncountr/plotting/heatmaps.py
src/ncountr/plotting/pathway_plots.py
src/ncountr/plotting/qc_plots.py
src/ncountr/plotting/style.py
tests/__init__.py
tests/conftest.py
tests/test_config.py
tests/test_de.py
tests/test_normalize.py
tests/test_qc.py
tests/test_rcc.py