Metadata-Version: 2.1
Name: celligner
Version: 0.9.3
Summary: A useful module for alligning cell lines to tumors
Home-page: https://github.com/BroadInstitute/celligner
Author: Jeremie Kalfon
Author-email: jkobject@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.5
Description-Content-Type: text/markdown
Requires-Dist: umap-learn (>=0.3)
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: contrastive (>=1.1)
Requires-Dist: Broad-genepy (>=1.1.2)
Requires-Dist: scikit-learn (>=0.24)
Requires-Dist: umap (>=0.1)
Requires-Dist: scanpy (>=1.8)
Requires-Dist: anndata (>=0.7)
Requires-Dist: scipy
Requires-Dist: bokeh (>=2.3)
Requires-Dist: louvain
Requires-Dist: pynndescent
Provides-Extra: test
Requires-Dist: pytest ; extra == 'test'
Requires-Dist: coverage ; extra == 'test'
Requires-Dist: flake8 ; extra == 'test'
Requires-Dist: black ; extra == 'test'
Requires-Dist: isort ; extra == 'test'
Requires-Dist: pytest-cov ; extra == 'test'
Requires-Dist: codecov ; extra == 'test'
Requires-Dist: mypy ; extra == 'test'
Requires-Dist: gitchangelog ; extra == 'test'
Requires-Dist: mkdocs ; extra == 'test'

# Celligner

![](docs/typical_celligner.webp)

celligner is a computational project to align multiple cancer datasets across sequencing modalities, tissue conditions (media, perturbations..) and format (CL/tumor/organoids/spheroids)

see our latest paper on aligning CCLE cell lines with TCGA tumors:
[2020 paper](https://www.nature.com/articles/s41467-020-20294-x)


## Install

> TO see the old R package installation instruction, see the `R/`folder.

`pip install celligner`

a dockerized version is available at `jkobject:pycelligner`

## for developers

see `CONTRIBUTING.md`

## run Celligner

see `docs/Celligner_demo.[html|pdf]` for an example of usage.

## Multidataset alignment

see `docs/Celligner_demo.[html|pdf]` for an example of usage.

one can use addToFit(), addToPredict() depending on whether they want to align their dataset to another or align another dataset to theirs.

if you have a very small dataset and want to align to CCLE or CGA, use the parameter `doAdd=True` in order to not rerun the entire pipeline and use cached information.

# R celligner

for the original R version of celligner, please check the R/README.md file here: [https://github.com/broadinstitute.org/celligner/tree/master/R/README.md](https://github.com/broadinstitute.org/celligner/tree/master/R/README.md)

---

Please use _github issues_ for any problem related to the tool.

Maintainers:

Jérémie Kalfon @jkobject
James McFarland
Javad Noorbak @jnoorbak

Created by:

Allie Warren @awarren

