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

5 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?