Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python.

ABSTRACT:

Summary

Transcript quantification tools efficiently map bulk RNA sequencing (RNA-seq) reads to reference transcriptomes. However, their output consists of transcript count estimates that are subject to multiple biases and cannot be readily used with existing differential gene expression analysis tools in Python.Here we present pytximport, a Python implementation of the tximport R package that supports a variety of input formats, different modes of bias correction, inferential replicates, gene-level summarization of transcript counts, transcript-level exports, transcript-to-gene mapping generation, and optional filtering of transcripts by biotype. pytximport is part of the scverse ecosystem of open-source Python software packages for omics analyses and includes both a Python as well

SUBMITTER: Kuehl M 

PROVIDER: S-EPMC11629965 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature