News, Tutorials, Tips and Tricks

BioBam Achieves ISO 27001 Recertification

In recent years, we have been updating our ISO 27001 certification status since its initial achievement in 2020. Since then, the BioBam team has been dedicated to maintaining high standards of quality and security during each annual review. We are pleased to announce that BioBam has now been recertified as a secure and responsible organization by the ISO 27001 standard.

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BioBam Trip to PAG in San Diego

  The BioBam team has recently returned from the 31st International Plant and Animal Genome Conference (PAG) in sunny California. Once again, PAG proved to be a great place for sharing, learning, and presenting the latest features of our bioinformatics solutions.   We showed OmicsBox to many attendees and hopefully improved their understanding of its rich set of features and

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Gene Set Analysis of GWAS data with MAGMA

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

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Long-Read Sequence Alignment with Minimap2

  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

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STARsolo Single-cell Quantification in OmicsBox

  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

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cutadapt omicsbox

Demultiplexing with Cutadapt in OmicsBox

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

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Monocle3 in OmicsBox: scRNA Seq trajectory interference

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

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New Release of OmicsBox 3.1

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.

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Biobam’s Sustainable Journey to ISMB/ECCB 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

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