Metadata-Version: 2.1
Name: ann-gsea
Version: 0.0.0
Summary: ann-gsea - integrate GSEA molecular signatures with AnnData
Home-page: UNKNOWN
Author: Michael E. Vinyard - Harvard University - Massachussetts General Hospital - Broad Institute of MIT and Harvard
Author-email: mvinyard@broadinstitute.org
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Programming Language :: Python :: 3.6
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >3.6.0
Description-Content-Type: text/markdown
Requires-Dist: anndata (>=0.7.8)

# annsig
An API for annotating single-cell AnnData with Molecular Signatures from [MSigDB](https://www.gsea-msigdb.org/gsea/msigdb/)

To use: 

### Step 1. Install

To install with the latest release from **PYPI**:
```BASH
pip install annsig
```

alternatively, install the development version:
```BASH
git clone https://github.com/mvinyard/annsig

cd annsig; pip install -e .
```

### Step 2. Register and download MSigDB

[link](http://www.gsea-msigdb.org/gsea/downloads.jsp#msigdb)
Developed with: `"msigdb.v7.4.symbols.gmt"` (Currently the latest version)

### Step 3. Example usage

```python
import ann_gsea as gsea

db = gsea.MSigDB()
db.load()
```

```python
db.search()
```

```python
db.fetch()
```

[link](http://www.gsea-msigdb.org/gsea/downloads.jsp#msigdb)
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.


