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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

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.

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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!

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

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Reference-free analysis of long-read RNA sequencing for non-model species

OmicsBox in a New Scientific Publication on Sorghum Stress Responses

LongTREC Secondments at BioBam: Advancing Long-Read Transcriptomics Through Collaboration

Cell Type Prediction with CellKb

OmicsBox 3.4: CellKb’s Advanced Cell-Type Annotation

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