PT - JOURNAL ARTICLE AU - Charles K. Fisher AU - Aaron M. Smith AU - Jonathan R. Walsh TI - Who is this gene and what does it do? A toolkit for munging transcriptomics data in python AID - 10.1101/299107 DP - 2018 Jan 01 TA - bioRxiv PG - 299107 4099 - http://biorxiv.org/content/early/2018/04/10/299107.short 4100 - http://biorxiv.org/content/early/2018/04/10/299107.full AB - 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.