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Predict coding regions within transcripts in OmicsBox with TransDecoder

Enrique Presa February 4, 2023

Most transcripts assembled from eukaryotic and prokaryotic RNA-Seq data are expected to code for proteins. The most practical procedure to identify likely coding transcripts is a sequence homology search, such as by BLASTX, against sequences from well-annotated and related species. Predicting coding regions is crucial to determine the molecular role that transcripts play in the cell. Unfortunately, such well-annotated nearby

BioBam is part of INTERCEPT-MDS, a European ITN

Paula Cubilles December 13, 2022

We are very proud to be part of the European Project INTERCEPT-MDS, a highly competitive international training network (ITN) that seeks to advance cancer research and have a high impact on future generations of researchers. In this article, you can learn more about ITNs in general and this initiative in particular. What is an ITN? An ITN is a training

BioBam accomplishes ISO 27001 certification

Stefan Götz October 28, 2022

At BioBam, we are strongly committed to ensuring that all of our bioinformatics solutions comply with the highest data security standards. We aim to provide the highest security for our customer’s data, which we store and protect. Once again, BioBam can proudly announce that we have achieved ISO 27001 certification for Information Security and Privacy.

Cell-Type Identification via Functional Enrichment Analysis of Single-Cell RNA-Seq Data

Marta Benegas Coll October 13, 2022

Single-cell RNA sequencing (scRNA-seq) has proven its usefulness in deciphering biological processes. Since it allows the study of samples at the cell level, it provides a more detailed view of the underlying biology. A nearly mandatory step in any scRNA-seq analysis is to identify the cell types present in the analyzed samples so further biological insights can be obtained.

BioBam at the ECCB 2022

Paula Cubilles October 5, 2022

From the 18th to the 21st of September, the BioBam team had the opportunity to take part in one of the largest European conferences on computational biology. The Spanish National Bioinformatics Institute (INB/ELIXIR-ES) and the Barcelona Supercomputing Center (BSC) welcomed bioinformatics and bioscientist from all over the world to the city of Sitges (Barcelona, Spain) to participate in the 21st

OmicsBox 2.2 Release

Paula Cubilles September 8, 2022

We are happy to announce the latest update of OmicsBox 2.2. After several months of intensive work we are finally ready to present the new version of BioBam’s bioinformatics solution. OmicsBox 2.2 comes with new Single Cell and Long Read Data Analysis Features and many other platform improvements. OmicsBox continues improving to become the most efficient, powerful and user-friendly bioinformatics

Tutorial: Single-Cell RNA-Seq Differential Expression Analysis

Marta Benegas Coll September 4, 2022

The differential expression (DE) analysis has been used in bulk RNA-seq analysis for many years. It allows us to statistically measure 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 between samples and conditions are

BAM File Quality Control

David Seide August 24, 2022

Transcriptome sequencing (RNA-Seq) produces big amounts of valuable information on all transcribed elements in the genome. With RNA-Seq, researchers can interrogate the transcriptome to profile gene expression, uncover alternative splicing, and identify novel and discard aberrant transcripts and coding variants, among others. The resulting BAM Files are the source of information for all proceeding step

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

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Predict coding regions within transcripts in OmicsBox with TransDecoder

BioBam is part of INTERCEPT-MDS, a European ITN

BioBam accomplishes ISO 27001 certification

Cell-Type Identification via Functional Enrichment Analysis of Single-Cell RNA-Seq Data

BioBam at the ECCB 2022

OmicsBox 2.2 Release

Tutorial: Single-Cell RNA-Seq Differential Expression Analysis

BAM File Quality Control

scRNA-seq Differential Expression with EdgeR

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