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Pathway Analysis with OmicsBox: Analyzing a Salamander Limb Regeneration Transcriptomics Dataset

Carlos Martinez May 28, 2023

The functional interpretation of differentially expressed genes obtained from RNA-seq data is a critical step in elucidating the intricate biological mechanisms underlying complex biological processes. Pathway analysis has emerged as a powerful approach to gaining insights into the coordinated interactions among genes within biological pathways. However, a major challenge in pathway analysis lies in the availability of annotation data, which

BioBam at the BIO-IT World 2023

Paula Cubilles May 23, 2023

The vibrant city of Boston recently hosted the highly anticipated BIO-IT World Conference. The BIO-IT is a premier gathering of industry professionals and innovators at the forefront of bioinformatics and computational biology. At our booth (we were #1 nevertheless!) we showcased OmicsBox, our user-friendly bioinformatics solution that simplifies data analysis and interpretation. Through live demonstrations, we showed how OmicsBox

Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2

Enrique Presa May 22, 2023

Transcriptome reconstruction is a challenging bioinformatic problem. The development of long-read sequencing technologies has made it easier to solve this issue thanks to the possibility of having transcripts entirely contained in a read. In addition, different algorithms have emerged to generate transcriptomes from long-read datasets, such as FLAIR and StringTie2. Both tools can be used for transcriptome reconstruction with long-read data.

Genetic Variation Exploration in Non-Model Organisms with OmicsBox

Enrique Presa May 1, 2023

The study of genetic variation is fundamental in genomics research as it enables the comprehension of mutation causes and effects in the diversity of life. However, research in this field is well-developed in model organisms, while non-model organisms lack sufficient guidance for a consistent variant analysis pipeline. OmicsBox is a robust tool for investigating genetic variation in non-model organisms, facilitating

GWAS with OmicsBox

Enrique Presa April 24, 2023

Genome-Wide Association Studies (GWAS) are a valuable approach to investigating the relationship between genetic variations and phenotypic traits. However, due to many different analysis options, performing GWAS can be challenging, especially for researchers without a strong background in statistics or bioinformatics. OmicsBox’s Genetic Variation Module provides a solution by offering a user-friendly interface to powerful analysis tools. It includes

KEGG Pathways in OmicsBox

Paula Cubilles March 22, 2023

This article explains how to analyse your data with the help of KEGG Pathways with OmicsBox. The free KEGG pathway app can be installed via the App Manager.

Quality Assessment of DNA-Seq De Novo Assemblies using QUAST

Marta Benegas Coll March 7, 2023

Genetic Variation studies often involve analyzing samples from a previously studied species. For instance, it is of interest to examine genomes of various cultivars, strains, or populations of the same species. In such cases, it may be necessary to perform de novo DNA-Seq assembly to obtain the genome of the sequenced organisms, even if a reference genome is available. To

LongTREC – BioBam member of a new ITN initiative

Paula Cubilles March 6, 2023

The European Union’s ITN initiative provides funding and hosting opportunities for Ph.D. students from around the world. As previously noted in one of our earlier posts, the ITN brings together some of the most prestigious institutions in the European Union to work on innovative research projects. Today we are pleased to present you the LongTREC project. Its primary objective is

OmicsBox 3.0 Release: New Module and Features

Paula Cubilles February 15, 2023

Once again we are pleased to announce the latest update of OmicsBox 3.0. The whole BioBam team has worked to bring the new version of the BioBam bioinformatics solution to life. We proudly present the Genetic Variation Module as the highlight of OmicsBox 3.0. This module enables variant calling, filtering, and annotation, as well as the association of genetic variations

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Pathway Analysis with OmicsBox: Analyzing a Salamander Limb Regeneration Transcriptomics Dataset

BioBam at the BIO-IT World 2023

Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2

Genetic Variation Exploration in Non-Model Organisms with OmicsBox

GWAS with OmicsBox

KEGG Pathways in OmicsBox

Quality Assessment of DNA-Seq De Novo Assemblies using QUAST

LongTREC – BioBam member of a new ITN initiative

OmicsBox 3.0 Release: New Module and Features

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BioBam at LongTREC meeting in Sweden

OmicsBox in SEBiBC First Congress: End-to-end Single Cell Data Analysis Poster

Genome Completeness Assessment with BUSCO

New Taxonomy Databases in OmicsBox

Combining Transcriptomes with TAMA Merge

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