It is possible to run Blast only on the differential expressed genes and not on all the data with OmicsBox. One has to select only those sequences that have differential expressed genes in the OmicsBox project.First, make sure that the name of the sequences in the project match the ones from the differential expression results.
How to combine pairwise differential expression results with a functional annotation project in OmicsBox.
Once differential expression results are retrieved, it could be interesting to assign functional annotations to the differentially expressed genes and visualize the results in a single project. This is possible in OmicsBox.
One of the most common applications of RNA-seq is to estimate gene and transcript expression. It starts with the alignment or mapping of reads and there are two possible alternatives: mapping to the genome when a reference sequence is available or mapping to the transcriptome (e.g. de novo assembled transcriptome). Reads may map uniquely or could be multi-mapped reads, while
This article explains how to start functional enrichment analysis of pairwise differential genes in Blast2GO.
This article explains how to create ID lists of either Blast results or differential expressed genes in Blast2GO.
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 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
(Release Date: 13/09/2016) We are very happy to announce the release of Blast2GO 4. This new version contains many new bioinformatic features like Differential Expression Analysis, Gene Finding or Gene Set Enrichment Analysis. Blast2GO will update automatically if activated. Otherwise please download the latest version online from here. Feedback, questions, as well as feature requests, are most welcome. Please write
Tips And Tricks
Helpful Features, Tips and Tricks
Use Cases, Reviews, Tutorials
Product Tutorial, Quickstarts, New Features, etc.