gsnetact 0.0.1

The pathway scoring algorithm as a python package.

GSNetAct

Please cite this repository if you use this code in your work.

Prerequisites

• Tested only on python 3.12, should work python 3.7+
• Numpy
• Scanpy
• Dataclasses
• Json
• Scikit-learn (Should come with scanpy but still)

Installing

• Clone the repository from this source.

git clone https://github.com/BMGLab/pathway_scorers

• Then inside the project directory, do

pip install .

The package should be installed. You can use the -e flag for automatic updates.

Usage

You can use every part of this package to develop a further approach to this algorithm. But for simple analysis, a basic use case below would be :

#!/usr/bin/env python

from gsnetact import createAdataObject

import pandas as pd

json_file_path = "Your Json File Path Containing Genesets and Their Relations."
annData_path = "Your Expressions File Path, Containing Gene Expression Data That Can Be Interpreted as AnnData by Scanpy."

analysis_result_as_annData = createAdataObject(annData_path,json_file_path,normalized=True)

df = pd.DataFrame(analysis_result_as_annData.X)
df.columns = analysis_result_as_annData.var

df.to_csv("output.csv",sep="\t")

This code firstly imports the createObject from the package, which is used for creating an AnnData object using the analysis results. Then, we specify our file paths. The pathwayScoring package needs two file inputs, one gene expression data file, and one JSON file that contains genesets and their relations. We then call the createObject function to get our files, analyzes them using the pathwayScoring's respected algorihm and creates an AnnData object using scanpy. We can use this object any way we want, for here it is used for creating a csv file that contains the scorings.

For further explanation, check the test files in test/ folder.

File Format for Genesets

The file that contains genesets and their relations has to be like this :

{
	"GeneSet1": {
		"Gene1": {
			"Gene2": 0.35,
			"Gene3": 0.77,
			"Gene4": 0.16
		},
		"Gene2": {
			"Gene1": 0.35,
			"Gene3": 0.51
		},
		"Gene3": {
			"Gene1": 0.77,
			"Gene2": 0.51,
			"Gene4": 0.40
		},
		"Gene4": {
			"Gene1": 0.16,
			"Gene3": 0.40
		}
	},
	"GeneSet2": {
		"Gene1": {
			"Gene2": 0.99
		},
		"Gene2": {
			"Gene1": 0.99
		}
	}
}

Here, GeneSet1 looks like this:

You can create this format easily though, check below.

JSON Creator Tool

You can create the needed JSON file containing genesets with the data from msigdb databases. All you need to do is :

#!/usr/bin/env python

from gsnetact import makeJson

makeJson("Path to your msigdb JSON file.","Name of the JSON file containing genesets, name them whatever you want.")

The makeJson function takes your geneset names from msigdb data and finds the relations between individual genes using the STRING database.