TY - JOUR
T1 - Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python
AU - Kuehl, Malte
AU - Wong, Milagros N
AU - Wanner, Nicola
AU - Bonn, Stefan
AU - Puelles, Victor G
PY - 2024/12/1
Y1 - 2024/12/1
N2 - 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 as a command-line interface. With pytximport, we propose a bulk RNA-seq analysis workflow based on Bioconda and scverse ecosystem packages, ensuring reproducible analyses through Snakemake rules. We apply this pipeline to a publicly available RNA-seq dataset, demonstrating how pytximport enables the creation of Python-centric workflows capable of providing insights into transcriptomic alterations.
AB - 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 as a command-line interface. With pytximport, we propose a bulk RNA-seq analysis workflow based on Bioconda and scverse ecosystem packages, ensuring reproducible analyses through Snakemake rules. We apply this pipeline to a publicly available RNA-seq dataset, demonstrating how pytximport enables the creation of Python-centric workflows capable of providing insights into transcriptomic alterations.
UR - http://www.scopus.com/inward/record.url?scp=85212161107&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btae700
DO - 10.1093/bioinformatics/btae700
M3 - Journal article
C2 - 39565903
SN - 1367-4811
VL - 40
JO - Bioinformatics
JF - Bioinformatics
IS - 12
M1 - btae700
ER -