The “Create Count Table” feature of OmicsBox/Blast2GO allows quantifying the gene expression of RNA-seq datasets. This video shows step-by-step how to create a count table of raw reads and explains in detail different concepts of expression quantification. The available parameters are inspired by the popular HTSeq Python Package (reference below).
The Time Course Expression Analysis tool allows performing a differential expression analysis of expression data arising from a time course RNA-seq experiment. This application is based on the maSigPro Bioconductor package, which implements a two-step regression strategy to detect genes with significant temporal expression changes and significant differences between experimental groups. This video shows the analysis of count data coming
The Pairwise Differential Expression Analysis tool is designed to perform differential expression analysis of count data arising from an RNA-seq experiment. The application, which is based on the software package “edgeR”, allows the identification of differentially expressed genes between two experimental conditions by applying quantitative statistical methods. This video shows the performance of a pairwise differential expression analysis in which
A simple use-case comparing OmicsBox with R chunks for Time Course Expression Analysis The Blast2GO feature “Time Course Expression Analysis” is designed to perform time-course expression analysis of count data arising from RNA-seq technology. Based on the software package ‘maSigPro’, which belongs to the Bioconductor project, this tool allows the detection of genomic features with significant temporal expression changes and
A simple use-case comparing OmicsBox with R chunks The OmicsBox feature “Pairwise Differential Expression Analysis” is designed to perform differential expression analysis of count data arising from RNA-seq technology. This tool allows the identification of differential expressed genes considering two different conditions based on the software package ‘edgeR’, which belongs to the Bioconductor project. This use case shows the basic
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