Welcome to GSForge’s documentation!

Note

This is a pre-release version of GSForge, and some function names may not be stable.

GSForge provides the following utilities to aid in collating and analyzing feature selection results from expression count matrices:

  1. Data structures that index expression and annotation in a single file.

  2. A common interface for membership set selection operators.

  3. Plotting functions for comparing expression as well as set intersections.

It aims to provide tools that are species-agnostic, that allow a practicing researcher to more easily collate and compare selection results across a variety of methods (from both R and Python). GSForge is not an analysis tool itself, but the documentation provides example implementations.

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Installation

GSForge works with Python 3.7+. It is currently only tested on Linux.

Install via pip

pip install GSForge

Install via Github source

Clone the repository:

git clone git@github.com:SystemsGenetics/GSForge.git

Then install locally via pip:

pip install ./GSForge

Overview

You should consider using GSForge when you have:

  • More than one feature selection method.

  • Many parameter sets to compare using one (or more) feature selection methods.

  • More than one normalization to explore.

  • You have a feature selection method that is non-deterministic.

You should seriously consider using GSForge if you find yourself in more than one of the above categories. The general workflow is then:

  1. Import Data and create an AnnotatedGEM.

  2. Find or select genes of interest and store the results in a Gene Set.

  3. Collate both the AnnotatedGEM and the sets of interest in a GeneSetCollection.

  4. Use the Interface to access and compare sets.

User Guide / Tutorial:

Reference Examples:

Walkthroughs: