ann-gsea - integrate GSEA molecular signatures with AnnData
Project description
annsig
An API for annotating single-cell AnnData with Molecular Signatures from MSigDB
To use:
Step 1. Install
To install with the latest release from PYPI:
pip install annsig
alternatively, install the development version:
git clone https://github.com/mvinyard/annsig
cd annsig; pip install -e .
Step 2. Register and download MSigDB
link
Developed with: "msigdb.v7.4.symbols.gmt"
(Currently the latest version)
Step 3. Example usage
import ann_gsea as gsea
db = gsea.MSigDB()
db.load()
db.search()
db.fetch()
link
Developed with: "msigdb.v7.4.symbols.gmt"
(Currently the latest version)
Instructions from the MSigDB website on how to cite their resource:
To cite your use of the Molecular Signatures Database (MSigDB), a joint project of UC San Diego and Broad Institute, please reference Subramanian, Tamayo, et al. (2005, PNAS) and one or more of the following as appropriate: Liberzon, et al. (2011, Bioinformatics), Liberzon, et al. (2015, Cell Systems), and also the source for the gene set as listed on the gene set page.
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