Who is this gene and what does it do? A toolkit for munging transcriptomics data in python

Transcriptional regulation is extremely complicated. Unfortunately, so is working with transcriptional data. Genes can be referred to using a multitude of different identifiers and are assigned to an ever increasing number of categories. Gene expression data may be available in a variety of units (e.g, counts, RPKMs, TPMs). Batch effects dominate signal, but metadata may not be available. Most of the tools are written in R. Here, we introduce a library, genemunge, that makes it easier to work with transcriptional data in python. This includes translating between various types of gene names, accessing Gene Ontology (GO) information, obtaining expression levels of genes in healthy tissue, correcting for batch effects, and using prior knowledge to select sets of genes for further analysis. Code for genemunge is freely available on Github (http://github.com/unlearnai/genemunge).

Enter your email address to download paper.

Click the link to begin download.
Oops! Something went wrong while submitting the form.
Blog

Embracing Innovation to Move Forward

Podcasts

Your Digital Twin - UnlearnAI

Podcasts

Using AI Digital Twins for Drug Testing

Dr. Charles Fisher, CEO of Unlearn AI, discusses creating digital clones by using artificial intelligence for use in clinical drug trials.
A fascinating approach to the problem of how to make clinical trials more efficient, and understand more about what may be possible with more and better patient data.
At Unlearn, our goal is to use the data available from historical trials, to generate new evidence to inform and advance research.