reanalyzerGSE: tackling the everlasting lack of reproducibility and reanalyses in transcriptomics
reanalyzerGSE: tackling the everlasting lack of reproducibility and reanalyses in transcriptomics
ABSTRACT SummaryIn the current context of transcriptomics democratization, there is an unprecedented surge in the number of studies and datasets. However, advances are hampered by aspects such as the reproducibility crisis, and lack of standardization, in particular with scarce reanalyses of secondary data. reanalyzerGSE, is a user-friendly pipeline that aims to be an all-in-one automatic solution for locally available transcriptomic data and those found in public repositories, thereby encouraging data reuse. With its modular and expandable design, reanalyzerGSE combines cutting-edge software to effectively address simple and complex transcriptomic studies ensuring standardization, up to date reference genome, reproducibility, and flexibility for researchers. Availability and implementationThe reanalyzerGSE open-source code and test data are freely available at both https://github.com/BioinfoIPBLN/reanalyzerGSE and 10.5281/zenodo.XXXX under the GPL3 license.Supplementary data are available.
Fern¨￠ndez-Rengel Iv¨￠n、Terr¨?n-Camero Laura C、Delgado Mario、Andr¨|s-Le¨?n Eduardo、Ruiz Jos¨| L、Gonzalez-Rey Elena、Castillo-Gonz¨￠lez Julia
Institute of Parasitology and Biomedicine ?°L¨?pez-Neyra?±, CSIC (IPBLN-CSIC)Institute of Parasitology and Biomedicine ?°L¨?pez-Neyra?±, CSIC (IPBLN-CSIC)Institute of Parasitology and Biomedicine ?°L¨?pez-Neyra?±, CSIC (IPBLN-CSIC)Institute of Parasitology and Biomedicine ?°L¨?pez-Neyra?±, CSIC (IPBLN-CSIC)Institute of Parasitology and Biomedicine ?°L¨?pez-Neyra?±, CSIC (IPBLN-CSIC)Institute of Parasitology and Biomedicine ?°L¨?pez-Neyra?±, CSIC (IPBLN-CSIC)Institute of Parasitology and Biomedicine ?°L¨?pez-Neyra?±, CSIC (IPBLN-CSIC)
生物科学研究方法、生物科学研究技术计算技术、计算机技术分子生物学
Fern¨￠ndez-Rengel Iv¨￠n,Terr¨?n-Camero Laura C,Delgado Mario,Andr¨|s-Le¨?n Eduardo,Ruiz Jos¨| L,Gonzalez-Rey Elena,Castillo-Gonz¨￠lez Julia.reanalyzerGSE: tackling the everlasting lack of reproducibility and reanalyses in transcriptomics[EB/OL].(2025-03-28)[2025-05-01].https://www.biorxiv.org/content/10.1101/2023.07.12.548663.点此复制
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