News, Tutorials, Tips and Tricks

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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BioBam Student Scholarship – Apply Now!

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

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

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BioBam at the BIO-IT World 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

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Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2

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 to have 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.

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genetic variaton

Genetic Variation Exploration in Non-Model Organisms with OmicsBox

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 serves as a robust tool for investigating genetic variation in non-model organisms,

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Easy GWAS with OmicsBox

GWAS with OmicsBox

Genome-Wide Association Studies (GWAS) is 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 a

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