General genetics/genomics utilities.
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.
- pandas shotrcuts:
- 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
- Docs: https://app.netlify.com/sites/genetools
- Two new functions to customize tick labels on any existing plot:
wrap_tick_labels: add text wrapping
add_sample_size_to_labels: add group sample sizes with a
- Make writing PDF figures a deterministic process and make the PDF text editable.
- Scatterplot improvements:
- Adjust default marker shape and size to work better for most plots.
- Adjust HueValueStyle so that an explicit marker size is not specified there, only a marker size scaling factor. The scatterplot itself is responsible for defining the base marker size, while the palette of HueValueStyles should be drawable at any marker size.
- Change legends so that only one marker is drawn to indicate a group's style.
- Improve scatter plots and stacked bar plots.
HueValueStylefor granular styling of each hue.
- Centered log ratio (CLR) normalization for Cite-seq protein data.
- Pandas helpers for easier normalization
- Far faster implementation of
- Global submodule import (no longer need to import submodules individually)
- First release on PyPI.
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