Gene Ranker

This python CLI tool can rank genes based on their differential expression between a 'case' and a 'control' status, from most up-regulated to most down-regulated, with a variety of metrics.

This is not a differential expression analysis, as no p-values are computed since no statistical test is used. It is just meant to give each gene a 'rank' and a rank value in order to run other statistical methods such as pre-ranked GSEA.

Input data should be the base-2 logarithm of 1 + read counts (i.e log2(counts + 1)). The program un-logs the data when appropriate (e.g. running DESeq2).

Currently supported ranking methods:

• Fold Change: The fold_change method computes a simple difference of average fold changes between the case and controls.
• Cohen's d: The cohen_d metric computes Cohen's d between the different expression values of each gene.
• DESeq2 Shrunk Log Fold Change: Uses DESeq2's LFC shrinking method to compute LFCs, and uses them as ranking metric. This uses PyDESeq2, so the input data is always normalized in the process.
• Signal to Noise ratio: Compute the signal to noise ratio between the control and case genes. This is roughly the mean divided by the variance of each gene.
• Baumgartner-Weiss-Schindler test statistic: Compute the BWS statistic for each gene. Uses a scipy primitive so it's much faster than using bws_test.

Most of these methods come with a normalized version, where the input is first normalized with the "mean of ratios" method (as implemented by DESeq2). They are usually named as norm_<method>. You can use generanker --list-methods for a list of all the methods.

Installation

Install Python and cargo. Install the prerequisite fast-cohen executable with:

cargo install --git https://github.com/MrHedmad/fast-cohen.git

Then, install the tool with:

# I suggest you do this in a virtual environment:
# python -m venv env && source env/bin/activate
python -m pip install git+https://github.com/TCP-Lab/gene_ranker.git

You may then use generanker from the command line. Use generanker --help for additional usage details.