Use Cases, Reviews, Tutorials Archives - Page 2 of 6

Combined Pathway Analysis with OmicsBox

Stefan June 8, 2021

Introduction A pathway analysis is an important step in the final biological interpretation of experimental results in most omics studies. For non-model species however this often becomes a difficult endeavor due to the lack of functional information. The Combined Pathway Analysis tool allows to identify pathways from multiple pathway databases for any set of sequences. In combination with differential expression

Metagenomics based In Silico Analysis of Antibiotic Resistome in Saltern

Mariana Monteiro March 10, 2021

This project shows how OmicsBox was used to functional annotate Moringa oleifera and to better understand the genome of the plant.

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.

Transcriptome analysis reveals important metabolic pathways of Allium sativum

Mariana Monteiro October 6, 2020

OmicsBox was used to perform the complete transcriptome analysis of Allium sativum. Enrichment analysis revealed important metabolic pathways.

Cloud Blast and Cloud Units: How to use resources wisely

Stefan September 30, 2020

This article describes how to run CloudBlast wisely. OmicsBox allows you to perform NCBI Blast searches using a cloud system for high-performance computing. This system runs jobs in parallel and autoscales depending on demand. To control usage we use so-called CloudUnits. These units represent computation time (cpu seconds) on the AWS infrastructure. At the moment only Blast and InterProScan consume

The functional annotation of the plant Moringa oleifera

Mariana Monteiro July 13, 2020

This project shows how OmicsBox was used to functional annotate Moringa oleifera and to better understand the genome of the plant.

COVID-19 Research Project in the US with OmicsBox Support

Mariana Monteiro June 11, 2020

Understanding the molecular differences that underlie the different COVID19 progression severity with Omic

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

Clustering redundant transcripts in OmicsBox with CD-HIT

Carlos Menor May 8, 2020

De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. However, with the advancement of next-generation sequencing technologies, the amount of available sequencing data is growing exponentially. Because of this, assembly algorithms often generate a large number of transcripts. Removing redundancy from such data could be crucial for reducing storage space,

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Combined Pathway Analysis with OmicsBox

Metagenomics based In Silico Analysis of Antibiotic Resistome in Saltern

Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

Transcriptome analysis reveals important metabolic pathways of Allium sativum

Cloud Blast and Cloud Units: How to use resources wisely

The functional annotation of the plant Moringa oleifera

COVID-19 Research Project in the US with OmicsBox Support

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

Clustering redundant transcripts in OmicsBox with CD-HIT

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