DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models.

ABSTRACT:

Background

RNAseq is nowadays the method of choice for transcriptome analysis. In the last decades, a high number of statistical methods, and associated bioinformatics tools, for RNAseq analysis were developed. More recently, statistical studies realised neutral comparison studies using benchmark datasets, shedding light on the most appropriate approaches for RNAseq data analysis.

Results

DiCoExpress is a script-based tool implemented in R that includes methods chosen based on their performance in neutral comparisons studies. DiCoExpress uses pre-existing R packages including FactoMineR, edgeR and coseq, to perform quality control, differential, and co-expression analysis of RNAseq data. Users can perform the full analysis, providing a mapped read expression data file and a

SUBMITTER: Lambert I 

PROVIDER: S-EPMC7216733 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature