RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing
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| Názov: | RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing |
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| Autori: | Sophiane G. Bouirdene, Simon Gotty, Mickaël Leclercq, Charles Joly-Beauparlant, Emeric Texeraud, Steve Bilodeau, Arnaud Droit |
| Zdroj: | Scientific Reports, Vol 15, Iss 1, Pp 1-9 (2025) |
| Informácie o vydavateľovi: | Nature Portfolio, 2025. |
| Rok vydania: | 2025 |
| Zbierka: | LCC:Medicine LCC:Science |
| Predmety: | Bulk RNA-seq, Transcriptomics, Snakemake pipeline, Gene expression, Variant calling, Cell deconvolution, Medicine, Science |
| Popis: | Abstract RNA sequencing (RNA-seq) is a widely used method in transcriptomics research, offering insights into gene expression, variant discovery, and, when deconvoluted, the cellular composition of complex tissues. However, existing RNA-seq pipelines frequently emphasize gene expression analysis and often lack cell deconvolution and variant calling. To address these limitations, we present RnaXtract, a comprehensive and user-friendly pipeline designed to maximize extraction of valuable information from bulk RNA-seq data. RnaXtract automates an entire workflow, encompassing quality control, gene expression quantification, variant calling, and the cell-type deconvolution. Built on the Snakemake framework, RnaXtract ensures robust reproducibility, efficient resource management, and flexibility to adapt to diverse research needs. The pipeline integrates state-of-the-art tools, from quality control to the new updates on variant calling and cell-type deconvolution tools such as EcoTyper and CIBERSORTx, enabling researchers to extract biological insights with precision. By providing an end-to-end solution for bulk RNA-seq, RnaXtract addresses critical gaps in existing workflows, empowering researchers to explore gene expression, genetic variation, and cellular heterogeneity within a single cohesive framework. |
| Druh dokumentu: | article |
| Popis súboru: | electronic resource |
| Jazyk: | English |
| ISSN: | 2045-2322 |
| Relation: | https://doaj.org/toc/2045-2322 |
| DOI: | 10.1038/s41598-025-16875-9 |
| Prístupová URL adresa: | https://doaj.org/article/25c4a6fce7194cd8821f785fd4524a6f |
| Prístupové číslo: | edsdoj.25c4a6fce7194cd8821f785fd4524a6f |
| Databáza: | Directory of Open Access Journals |
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Nájsť tento článok vo Web of Science | Abstrakt: | Abstract RNA sequencing (RNA-seq) is a widely used method in transcriptomics research, offering insights into gene expression, variant discovery, and, when deconvoluted, the cellular composition of complex tissues. However, existing RNA-seq pipelines frequently emphasize gene expression analysis and often lack cell deconvolution and variant calling. To address these limitations, we present RnaXtract, a comprehensive and user-friendly pipeline designed to maximize extraction of valuable information from bulk RNA-seq data. RnaXtract automates an entire workflow, encompassing quality control, gene expression quantification, variant calling, and the cell-type deconvolution. Built on the Snakemake framework, RnaXtract ensures robust reproducibility, efficient resource management, and flexibility to adapt to diverse research needs. The pipeline integrates state-of-the-art tools, from quality control to the new updates on variant calling and cell-type deconvolution tools such as EcoTyper and CIBERSORTx, enabling researchers to extract biological insights with precision. By providing an end-to-end solution for bulk RNA-seq, RnaXtract addresses critical gaps in existing workflows, empowering researchers to explore gene expression, genetic variation, and cellular heterogeneity within a single cohesive framework. |
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| ISSN: | 20452322 |
| DOI: | 10.1038/s41598-025-16875-9 |