gcell is a comprehensive toolkit for genomic data analysis, focusing on cell type-specific regulatory analysis, DNA and RNA sequence manipulation, protein structure prediction, and pathway analysis. It integrates various modules to facilitate the study of different aspects of gene expression regulation.
The long term goal of this package is to create a open-source, community-involved python-centric playground/tool-set for future AI Agent to discover new biology through predictive model.
- Celltype: Tools for cell type analysis, including gene expression and motif analysis. Basis for
get_modelinterpretation analysis. - DNA: Functions for DNA sequence manipulation, motif scanning, and track visualization.
- RNA: Classes for handling GENCODE gene annotations and GTF files.
- Protein: Functionality for protein domain analysis (Uniprot, InterPro) and AlphaFold2 predictions parsing as well as retrieve protein-protein interaction networks from the STRING database..
- Pathway: Tools for pathway (GO, KEGG, Reactome, etc.) analysis using gprofiler.
pip install git+https://github.com/GET-Foundation/gcell.git@main
gcell is open-source software licensed under the MIT License. See the LICENSE file for more details.