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.