found: HiDDEN implementation#

this repository provides an implementation of a method for refining case-control labels in single-cell -omics data, as decribed in Goeva et al, 2024

disclaimer#

API is subject to breaking changes under 0ver, no releases cut so far, breaking changes are pushed to main

planned future features / TODO#

  • support for more underlying data types within methods (e.g. zarr arrays, HDF5 arrays as matrix types, etc.)

  • native support for multinomial/ordinal condition labels (both in entrypoints and method implementations)

  • remove typechecker ignore comments where possible (e.g. via asserts and/or further type hints) & add necessity/safety explainers where missing

installation#

uv is used for package management and installation

found can be installed via the following command:

uv pip install 'git+ssh://git@github.com/goeva-lab/found'

alternatively, a docker/OCI image is provided at ghcr.io/goeva-lab/found (built according to instructions in ./Dockerfile and via the github workflow step build_docker), which provides a debian-based environment with both R and python found packages pre-installed.

this image can be downloaded via the following command (replace docker w/ podman/etc. as needed):

docker pull 'ghcr.io/goeva-lab/found'

R bridge#

an R package providing high-level bindings to the python package is provided, for more documentation on it, please see https://goeva-lab.ccbr.utoronto.ca/found/R. all materials below are regarding the python package.

documentation#

a build of the documentation is publicly available at: https://goeva-lab.ccbr.utoronto.ca/found/py.

to build it locally (and run associated notebooks), a copy of the repo must be downloaded, dev dependencies must be installed, and a kernel based on the configured venv must be installed:

git clone 'git@github.com:goeva-lab/found' && cd found
uv pip install -e '.[dev]'
uv run --no-sync --frozen -m ipykernel install --user --name found

sphinx is used to build a documentation website, which can be built and previewed locally at localhost:8000 via the following command (assuming current directory is a clone of this repository):

uv run --no-sync --frozen sphinx-autobuild './docs' './docs/_build/html' -b 'dirhtml' -n --watch './src'

note: this will run and execute all guide vignettes, which can be very computationally expensive. to avoid doing this, you can pass -D nb_execution_mode=off to the above sphinx-autobuild command as an additional argument.

development/contributing#

this project uses ruff for formatting and ty for linting.

please ensure that any contributions pass formatting/linting checks accordingly, as determined by ruff check and ty check.