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Gene Set Analysis of GWAS data with MAGMA

Enrique Presa October 19, 2023

The pursuit of genetic advancement in agricultural crops is a nuanced and ongoing scientific endeavor. The advent of Genome-Wide Association Studies (GWAS) marked a significant stride, offering a window into the intricate interplay between genetic variants and phenotypes. Yet, the scope of insights garnered through GWAS can be further enriched when coupled with refined analytical tools. The Gene Set Analysis

Long-Read Sequence Alignment with Minimap2

Enrique Presa October 16, 2023

Sequence alignment is an essential element of genomics research, playing a significant role in aiding scientists in deciphering the intricacies of genetic data. When confronted with the task of aligning long reads generated by Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) with precision and efficiency, scientists commonly opt for Minimap2 as their preferred tool (it is the most

STARsolo Single-cell Quantification in OmicsBox

Marta Benegas Coll October 11, 2023

What is scRNA-Seq Quantification? The first step for any Single-cell RNA-Seq analysis is to perform the quantification or, in other words, to obtain the gene expression values by cell. It is the input data for further analysis like Clustering, Trajectory, Cell-Cell Communication, Differential Expression, etc. Briefly, in order to obtain the expression values the sequencing reads are aligned to

Demultiplexing with Cutadapt in OmicsBox

David Seide October 5, 2023

Barcoding and demultiplexing in high-throughput sequencing experiments Barcoding, or indexing, is a widely used strategy in high-throughput sequencing experiments. This method enables the multiplexing of numerous samples in a single sequencing run by adding a unique DNA sequence to each sample before sequencing. During sequencing, the barcodes are read along with the DNA fragments, allowing the identification and split of

Monocle3 in OmicsBox: scRNA Seq trajectory interference

Priyansh Srivastava October 2, 2023

OmicsBox’s Single Cell Data Analysis encompasses a comprehensive range of steps, spanning read quantification, pre-processing, clustering, differential expression analysis, and even advanced analyses like trajectory analysis and functional enrichment. This blog post will focus on general trajectory inference using Monocle3 within OmicsBox. Pseudotime Analysis with Monocle3 Monocle3, developed by the Trapnell lab, is a scRNA-Seq data analysis toolkit written in

BioBam organizes Single-Cell Course

Paula Cubilles September 29, 2023

From September 27th to 29th, 2023, BioBam organized a Single-Cell Data Analysis Course as part of the Intercept-MDS Network Training Activities. The course was designed to offer a specialized educational program aimed at providing Ph.D. candidates within the network with essential skills for exploring the intriguing field of single-cell data analysis. Course Overview The three-day program immersed participants in the

New Release of OmicsBox 3.1

Paula Cubilles September 27, 2023

Empowering Researchers with Advanced End-to-End Analysis Tools for Single-Cell and Genetic Variation Studies. We’re thrilled to announce the much-anticipated arrival of OmicsBox 3.1, a release that brings significant improvements to single-cell data analysis with UMI-based technology support and introduces a functional enrichment tool for genetic variation analysis. It also enhances OmicsBox’s long-read transcriptome analysis options, making it a one-of-a-kind solution.

Biobam’s Sustainable Journey to ISMB/ECCB 2023

Paula Cubilles August 1, 2023

Cycling for Green Science In a remarkable commitment to sustainability, the Biobam team embarked on an adventure to ISMB/ECCB 2023 in Lyon. BioBam sponsored the #Cycling4GreenScience initiative, riding 300 kilometers from Avignon to Lyon, for raising awareness about eco-friendly practices in scientific research and communication. The #Cycling4GreenScience adventure was a journey for the Biobam team. Biking 300 kilometers through scenic

BioBam Student Scholarship – Apply Now!

Paula Cubilles June 20, 2023

Exciting news! We are thrilled to announce that for the next 3 months, starting from the 1st of July, students can apply to get a full-featured 6-month OmicsBox license. That’s right – we’re granting you access to the powerful tools and resources of OmicsBox to fuel your research endeavors. Whether you’re exploring genomics, transcriptomics, or metagenomics, this subscription will equip

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Gene Set Analysis of GWAS data with MAGMA

Long-Read Sequence Alignment with Minimap2

STARsolo Single-cell Quantification in OmicsBox

Demultiplexing with Cutadapt in OmicsBox

Monocle3 in OmicsBox: scRNA Seq trajectory interference

BioBam organizes Single-Cell Course

New Release of OmicsBox 3.1

Biobam’s Sustainable Journey to ISMB/ECCB 2023

BioBam Student Scholarship – Apply Now!

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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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