genetools: single-cell analysis recipes (work in progress)¶
Compare clustering results by computing co-clustering percentage.
Map marker genes against reference lists to find names for your clusters.
Split single cell barcodes conveniently.
Defensive pandas merging and concatenation methods with strict correctness checks.
Full documentation: https://genetools.maximz.com.
pip install --upgrade 'genetools[scanpy]'.
Or if you don’t use scanpy:
pip install --upgrade genetools.
git clone git://github.com/maximz/genetools cd genetools pip install --upgrade pip wheel pip install -r requirements_dev.txt pre-commit install
# lint make lint # one-time: generate test anndata, and commit so we have reproducible tests in CI rm -r data make regen-test-data # run tests locally # this is done in a debian-based docker image to ensure image style matches what Github Actions CI will produce make build-docker-test-image # whenever requirements_dev.txt change make test # generate baseline figures (also happens in docker) make regen-snapshot-figures # regenerate test data, and baseline figures (also happens in docker) make regen-test-data # run tests locally without docker, therefore omitting the snapshot tests make test-without-figures # docs make docs # bump version before submitting a PR against master (all master commits are deployed) bump2version patch # possible: major / minor / patch # also ensure CHANGELOG.md updated
Main: Github Actions