amhaslam / as-quant

Quantitation and visualization of differential alternative splicing events

AS-Quant generates the expression level of alternative splicing among two different biological conditions.

Installation

AS-Quant tool can be downloaded directly from github. User need to have python installed in their machine. It can work on Windows, Linux and Mac platform.

User will need to run the as-quant.py file in order to demonstrate the AS events.

$python3 as_quant.py

To generate plots for specific exon, user need to run makePlots.py and provide input in a specific pattern: chromName:geneName:start-end

$python3 make_plots.py

User manual

User manual for AS-Quant is available on github https://github.com/compbiolabucf/AS-Quant/blob/master/AS-Quant%20User%20Manual.pdf

Sample data

AS-Quant example data for mouse(mouse mm10) is included in the folder https://github.com/compbiolabucf/AS-Quant/tree/master/Sample_input_mouse. To run from scratch, user can use the sample data for quantization of AS events.

Citation

Please use the following information to cite.

Contact the Author

Naima Ahmed Fahmi: [email protected] Wei Zhang: [email protected]