https://github.com/gtca/chame
Chromatin analysis module
https://github.com/gtca/chame
atac-seq chromatin genome multiome ranges scatac-seq scverse
Last synced: about 1 month ago
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Chromatin analysis module
- Host: GitHub
- URL: https://github.com/gtca/chame
- Owner: gtca
- License: bsd-3-clause
- Created: 2022-05-11T00:46:03.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-04-28T23:27:53.000Z (5 months ago)
- Last Synced: 2025-04-28T23:44:17.121Z (5 months ago)
- Topics: atac-seq, chromatin, genome, multiome, ranges, scatac-seq, scverse
- Language: Python
- Homepage: https://gtca.github.io/chame
- Size: 1.65 MB
- Stars: 4
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
> `chame` is work in progress. Active contributions via code or feedback are welcome.
`chame` stands for a _chromatin analysis module_. It is being developed as a Python library for working with genomic ranges and chromatin accessibility in the [`scverse`](https://scverse.org/) ecosystem.
[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
Raw data input: [10X Genomics ARC](https://gtca.github.io/chame/examples/10x_io.html), [ArchR (arrow files)](https://gtca.github.io/chame/examples/archr_io.html).
Data model: [AnnData](https://github.com/scverse/anndata) and [MuData](https://github.com/scverse/mudata).
## Preprocessing and QC
TF-IDF / LSI. TSS enrichment, mono-nucleosome occupancy, etc.
## Methods
[Differential accessibility](https://gtca.github.io/chame/examples/chromvar.html), transcription factor activity, etc.
## Visualization
QC. Joint gene + peak visualisation.
---
# Other projects
1. [muon](https://github.com/scverse/muon)
1. [SnapATAC2](https://github.com/kaizhang/SnapATAC2)
1. [episcanpy](https://github.com/colomemaria/epiScanpy)
1. [ArchR](https://www.archrproject.com/)
1. [Signac](https://satijalab.org/signac/)