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scRNA-seq Differential Expression with EdgeR

Marta Benegas Coll August 15, 2022

Why Differential Expression Analysis with Single-cell RNA-seq data? The differential expression (DE) analysis has been used in bulk RNA-seq analysis for many years. It statistically measures changes in gene expression levels between different groups. With bulk RNA-seq analysis many cells are sequenced at the same time, so gene expression levels are commonly measured at the tissue level. Thus, the differences

Quality Assessment with LongQC

Adolfo Lopez August 4, 2022

Specific tools for a new generation of sequencing Third Generation Sequencing (TGS) is getting a notable increase in relevance by surpassing some of the limitations of NGS technologies. In that sense, the main feature of TGS is the capacity to produce much longer reads than NGS. These long reads facilitate the assembly of complex genomes and the study of alternative

Transcriptome Analysis with SQANTI3

Enrique Presa July 28, 2022

Transcriptome analysis is a challenging bioinformatic problem. In eukaryotic transcriptomes, alternative splicing and alternative polyadenylation are the most complex issues. Genome-wide analysis of alternative splicing has been studied with short-read RNA sequencing for a while. Nevertheless, this technology needs a subsequent assembly, which is difficult to be resolved in ambiguities in complex loci.

Dynamics of bacterial resistome associated based on metagenomics analysis

Paula Cubilles July 22, 2022

New BioBam Scholarship Supported Project – with OmicsBox. BioBam’s central mission is to provide the scientific community with accessible and user-friendly bioinformatics solutions to accelerate biological research.

Bioinformatic analysis of gene expressions involved in berries growth

Mariana Monteiro April 28, 2022

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

Mining Genes involved in Biodegradation of Tannery Wastes

Mariana Monteiro January 11, 2022

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

Biobam receives a grant from the Valencian Innovation Agency – AVI

Robert Nica September 23, 2021

We are proud to announce that we have received a grant from the Valencian Innovation Agency – AVI Our I+D+i project “EVOLUTION OF THE COMPANY’S CLOUD SYSTEM TOWARDS AN ADVANCED ELASTIC PLATFORM FOR HIGH-PERFORMANCE COMPUTING AND MASSIVE SEQUENCING DATA PROCESSING” has received a grant from the Valencian Innovation Agency (AVI) in the line L3 Industrial Doctorate (innodocto) to support

metatranscriptomics SortMeRNA OmicsBox rRNA ribosomal removal filtering

rRNA Removal with SortMeRNA in OmicsBox

David Seide July 8, 2021

Introduction RNA-seq data from metatranscriptomics NGS projects contains both coding and non-coding types of RNAs. Before any gene expression or taxonomic analysis, it is important to separate reads in families of messenger RNAs and ribosomal RNAs (rRNAs). SortMeRNA, first released in 2012, is a fast and accurate tool for filtering ribosomal RNAs in metatranscriptomics datasets. The core algorithm is based

Contaminant Removal with Bowtie2 in OmicsBox

Metagenomics Contaminant Removal with Bowtie

David Seide July 8, 2021

Introduction A common preprocessing step in metagenomics data analysis e.g. working with host-associated studies is to remove the host-related DNA from the sequencing data. This is often referred to as contamination removal. A common approach to isolate host-related reads is performing a read mapping against the host genome. Bowtie2 is the reference tool for this task. Since OmicsBox 2.0 this

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scRNA-seq Differential Expression with EdgeR

Quality Assessment with LongQC

Transcriptome Analysis with SQANTI3

Dynamics of bacterial resistome associated based on metagenomics analysis

Bioinformatic analysis of gene expressions involved in berries growth

Mining Genes involved in Biodegradation of Tannery Wastes

Biobam receives a grant from the Valencian Innovation Agency – AVI

rRNA Removal with SortMeRNA in OmicsBox

Metagenomics Contaminant Removal with Bowtie

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