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 ecosystem.

Documentation | Examples

Install chame

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

Functionality

I/O

Raw data input: 10X Genomics ARC, ArchR (arrow files).

Data model: AnnData and MuData.

Preprocessing and QC

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

Methods

Differential accessibility, transcription factor activity, etc.

Visualization

QC. Joint gene + peak visualisation.

---

Other projects

1. muon
2. episcanpy
3. SnapATAC2
4. ArchR
5. Signac