User Guide¶

Getting Started¶

Creating and working with an AnnotatedGEM¶

• AnnotatedGEM from pandas How to load your count and label .csv or .txt files into an xarray.Dataset using GSForge, and save them as a single netcdf (.nc) file for future use.

• GEM Normalization How to run and save different normalizations to the same AnnotatedGEM object.

Selecting Genes & Creating a GeneSet¶

• Selecting Genes with Boruta How to select genes based on a sample label using random forests via the Boruta algorithm.

Creating a GeneSetCollection and Analyzing Results¶

• GeneSet Analysis How to run a basic gene (feature) selection using random forests and the Boruta all-relevant feature selection algorithm.

Other Guides¶

• Plotting Guide Plotting examples by plot type.

• Workflow Guide Using nextflow to run many different boruta analyses.

• R-Integration Guide Integrating results from R packages into GeneSet objects.