Differential Expression Analysis Archives

Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

David Seide November 23, 2020

1. Introduction Juvenile rhesus macaques commonly suffer from idiopathic chronic diarrhea (ICD). This disease is characterized by inflammation of the colon and repeated bouts of diarrhea. It is a common cause of morbidity and mortality among macaques because it is unresponsive to drugs. The gut microbiome of macaques with ICD is characterized by abrupt changes when compared to healthy individuals.

Zeroing in on genes involved in courtship song variation in Laupala crickets

Mariana Monteiro June 9, 2020

OmicsBox Supported Project. Researchers: Hayden Waller, Cornell University, USA Background and Project Overview: One of the primary outcomes of speciation – the formation of new species – is the generation of pre-mating barriers that prevent or greatly reduce gene flow. Behavioral changes are perhaps the most potent in the early stages of speciation. In particular, the divergent evolution of sexual

How to run Blast of the differential expressed genes?

Mariana Monteiro December 10, 2019

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.

Combine differential expression results with functional annotation in OmicsBox

Jesus Gutierrez April 18, 2019

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.

Expression quantification and differential expression analysis

Carlos Menor November 20, 2018

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

Enrichment Analysis from pairwise differential expression results in OmicsBox

Mariana Monteiro November 13, 2018

This article explains how to start functional enrichment analysis of pairwise differential genes in Blast2GO.

How to create a gene list within OmicsBox to run the functional enrichment analysis

Mariana Monteiro November 13, 2018

This article explains how to create ID lists of either Blast results or differential expressed genes in Blast2GO.

Pairwise Differential Expression Analysis

Carlos Menor October 17, 2016

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

Pairwise Differential Expression Analysis

Carlos Menor September 26, 2016

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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Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

Zeroing in on genes involved in courtship song variation in Laupala crickets

How to run Blast of the differential expressed genes?

Combine differential expression results with functional annotation in OmicsBox

Expression quantification and differential expression analysis

Enrichment Analysis from pairwise differential expression results in OmicsBox

How to create a gene list within OmicsBox to run the functional enrichment analysis

Pairwise Differential Expression Analysis

Pairwise Differential Expression Analysis

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