Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data

• Published in: BMC bioinformatics Vol. 25; no. 1; p. 138
• Main Authors: Blumenkamp, Patrick, Pfister, Max, Diedrich, Sonja, Brinkrolf, Karina, Jaenicke, Sebastian, Goesmann, Alexander
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 29-03-2024; BioMed Central; BMC
• Subjects: Automation; Binomial distribution; Bioinformatics; Curare; Data analysis; Data processing; Data visualization; Datasets; Differential gene expression; Electronic data processing; FAIR; Gene expression; Gene Expression Profiling - methods; Generalized linear models; High-Throughput Nucleotide Sequencing - methods; Methods; Quality control; Reproducibility; Reproducibility of Results; Ribonucleic acid; RNA; RNA sequencing; RNA-Seq; Sequence Analysis, RNA - methods; Software; Software packages; Transcriptome; Transcriptomes; Workflow; Germany; FAIR; Differential gene expression; RNA-Seq; Reproducibility; Data visualization
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05761-2

Even though high-throughput transcriptome sequencing is routinely performed in many laboratories, computational analysis of such data remains a cumbersome process often executed manually, hence error-prone and lacking reproducibility. For corresponding data processing, we introduce Curare, an easy-to-use yet versatile workflow builder for analyzing high-throughput RNA-Seq data focusing on differential gene expression experiments. Data analysis with Curare is customizable and subdivided into preprocessing, quality control, mapping, and downstream analysis stages, providing multiple options for each step while ensuring the reproducibility of the workflow. For a fast and straightforward exploration and visualization of differential gene expression results, we provide the gene expression visualizer software GenExVis. GenExVis can create various charts and tables from simple gene expression tables and DESeq2 results without the requirement to upload data or install software packages. In combination, Curare and GenExVis provide a comprehensive software environment that supports the entire data analysis process, from the initial handling of raw RNA-Seq data to the final DGE analyses and result visualizations, thereby significantly easing data processing and subsequent interpretation.