Metadata-Version: 2.1
Name: chame
Version: 0.0.1.dev0
Summary: Chromatin accessibility module
Author: Danila Bredikhin, Max Frank
Maintainer-email: Danila Bredikhin <danila.bredikhin@embl.de>
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: anndata
Requires-Dist: mudata
Requires-Dist: scanpy
Requires-Dist: pybedtools
Requires-Dist: pysam
Requires-Dist: sphinx ; extra == "doc"
Requires-Dist: myst-parser ; extra == "doc"
Requires-Dist: sphinx-book-theme ; extra == "doc"
Requires-Dist: readthedocs-sphinx-search ; extra == "doc"
Requires-Dist: nbsphinx ; extra == "doc"
Requires-Dist: sphinx-automodapi ; extra == "doc"
Requires-Dist: sphinxcontrib-bibtex ; extra == "doc"
Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
Requires-Dist: pytest ; extra == "test"
Requires-Dist: pytest-cov ; extra == "test"
Project-URL: Documentation, https://gtca.github.io/chame
Project-URL: Home-page, https://github.com/gtca/chame
Project-URL: Source, https://github.com/gtca/chame
Provides-Extra: dev
Provides-Extra: doc
Provides-Extra: test

<img src="./docs/img/chame_logo.svg" data-canonical-src="./docs/img/chame_logo.svg" width="700"/>

`chame` is a Python module to work with genomic ranges and chromatin accessibility.
Part of [`scverse`](https://scverse.org/).

[Documentation](https://gtca.github.io/chame) | [Examples](https://gtca.github.io/chame/examples/)

# Install `chame`

```
pip install git+https://github.com/gtca/chame
```

# Functionality

## I/O

10X Genomics ARC, SnapATAC, ArchR (arrow files).

## Preprocessing and QC

TF-IDF / LSI. TSS enrichment, mono-nucleosome occupancy, etc.

## Plotting

Joint gene + peak visualisation.

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# Other projects

1. [muon](https://github.com/scverse/muon)
1. [episcanpy](https://github.com/colomemaria/epiScanpy)
1. [SnapATAC2](https://github.com/kaizhang/SnapATAC2)
1. [ArchR](https://www.archrproject.com/)
1. [Signac](https://satijalab.org/signac/)


