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Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

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.

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courtship song Laupala crickets

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

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

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How to run Blast of the differential expressed genes?

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.

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Expression quantification and differential expression analysis

Expression quantification and differential expression analysis

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

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Pairwise Differential Expression Analysis

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

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Pairwise Differential Expression Analysis

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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