RTrans: a pipeline for multi-way analysis of differential gene expression profiles

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George Sergeevich Krasnov1, Anastasiya Andreevna Kobelyatskaya2, Anastasiya Vladimirovna Snezhkina3, Vladislav Sergeevich Pavlov4, Elena Anatolevna Pudova5, Anna Victorovna Kudryavtseva6
1EIMB RAS, gskrasnov@mail.ru
2EIMB RAS, kaa.chel@mail.ru
3EIMB RAS, leftger@rambler.ru
4EIMB RAS, vladislav1pavlov@gmail.com
5EIMB RAS, pudova_elena@inbox.ru
6EIMB RAS, rhizamoeba@mail.ru

RNA-Seq is a widespread technique routinely used to reveal differentially expressed (DE) genes, splicing events and affected signaling pathways. Usually, RNA-Seq data analysis needs skills in programming and bioinformatics. We aimed at developing easy-to-use pipeline covering multiple aspects of DE analysis. Here we present RTrans pipeline aimed at evaluating differential gene expression, pathway enrichment, WGCNA co-expression analysis and visualization. It provides rapid analysis of read counts data including MANOVA, paired tests, non-parametric tests. RTrans represents a versatile pipeline facilitating DE analysis based on RNA-Seq and other quantitative data.

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Daniil Wiebe
Daniil Wiebe
4 years ago

Thank You for the brilliant work and report!
Almost all tools used in the Rtrans pipeline have dozens of parameters inappropriate values of which can seriously affect the result. Does Rtrans allow to set such parameter values in the excel workbook, or RTrans sets them automatically according to the input data features?

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8 months ago

RTrans: a pipeline for multi-way analysis of differential gene expression profiles

http://menatwork.se/portfolio/pretium-quis/

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2 months ago

RTrans: a pipeline for multi-way analysis of differential gene expression profiles

https://www.pferdeklinik-bargteheide.de/en/team/veterinarians/dr-volker-sill/volker-kl-2/