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The Influence of Clustering Quality on Cell Type Prediction Accuracy

Marta Benegas Coll August 5, 2025

Accurate cell type prediction is a crucial step in the interpretation of single-cell RNA-seq data, as downstream biological insights strongly depend on these predictions. However, most annotation strategies rely on an initial unsupervised clustering step that is sensitive to parameter choices, thus leading to substantial variation in cell grouping. While it is widely acknowledged that clustering quality influences downstream analyses,

Join & Call vs. Call & Join: Poster at ISMB/ECCB2025

Fabian Jetzinger August 4, 2025

The analysis of long-read RNA-sequencing data, such as from the platforms of Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT), can be rather complicated, and there are few well-established gold-standard tools in the field. This leads different researchers to choose different tools despite similar research objectives, which can lead to notable differences in their results. One crucial step in

BioBam at the LongTREC Summer School

Fabian Jetzinger July 18, 2025

Our team member and PhD student Fabian Jetzinger recently contributed to the organization of the LongTREC summer school, held at the Earlham Institute in Norwich, UK. The 4-day course, organized by the MSCA doctoral network LongTREC welcomed 27 participants from across Europe for an intensive introduction to bioinformatic analyses of long-read transcriptomics data. A diverse range of complex topics

Differences between Fisher’s Exact Test and GSEA for Functional Enrichment

Marta Benegas Coll July 8, 2025

A functional enrichment analysis is the procedure of identifying functions that are over- or under-represented among a set of genes and may have an association with an experimental condition (e.g., phenotype or drug treatment). Obtaining functional profiles for sets of genes helps to gain a better understanding of the underlying biological processes. Two common analyses to test for enrichment

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

Fabian Jetzinger February 3, 2025

With improvements in accuracy and steadily decreasing costs, long-read sequencing technologies, such as the platforms provided by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), have revolutionized the field of transcriptomics in recent years. Compared to short-read sequencing, which requires RNA fragmentation, long-read sequencing technologies can sequence RNA molecules in their entirety. This allows researchers to study the transcriptome

OmicsBox in a New Scientific Publication on Sorghum Stress Responses

Paula Cubilles January 31, 2025

At BioBam we are proud to see OmicsBox supporting scientific research. It is always rewarding to witness our users making significant advances in their respective fields and publishing their findings in esteemed journals such as Nature Scientific Data. These publications reinforce OmicsBox’s role as a valuable tool in bioinformatics, helping researchers analyze complex datasets with precision and efficiency. A

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

Paula Cubilles January 29, 2025

The LongTREC Marie Skłodowska-Curie Actions Doctoral Networks is an innovative European initiative that advances transcriptomics through Long-Read RNA Sequencing (lrRNA-seq). PhD candidates participating in LongTREC benefit from collaborative opportunities with public and industry partners, gaining invaluable expertise while developing advanced tools and workflows. As part of the LongTREC network, BioBam hosts secondments and offers an unique environment where academia meets

Cell Type Prediction with CellKb

Marta Benegas Coll January 23, 2025

Single-cell transcriptomics has revolutionized the way we understand complex biological systems. By enabling researchers to study gene expression at the resolution of individual cells, it uncovers cellular heterogeneity, reveals intricate developmental pathways, and provides insights into disease mechanisms. However, as powerful as single-cell RNA sequencing (scRNA-Seq) is, translating its immense data into meaningful biological insights remains a great challenge. One

OmicsBox 3.4: CellKb’s Advanced Cell-Type Annotation

Paula Cubilles January 13, 2025

Improved Metagenomics Classification, and Enhanced Long-Read Transcriptomics Pipelines We proudly present the OmicsBox Version 3.4 release that introduces a range of enhancements designed to address the evolving needs of modern genomics and transcriptomics research. A key highlight of OmicsBox 3.4 is the integration of CellKb, a robust cell-type prediction tool for single-cell RNA sequencing (scRNA-Seq) analysis. CellKb streamlines scRNA-Seq annotation

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The Influence of Clustering Quality on Cell Type Prediction Accuracy

Join & Call vs. Call & Join: Poster at ISMB/ECCB2025

BioBam at the LongTREC Summer School

Differences between Fisher’s Exact Test and GSEA for Functional Enrichment

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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The Influence of Clustering Quality on Cell Type Prediction Accuracy

Join & Call vs. Call & Join: Poster at ISMB/ECCB2025

BioBam at the LongTREC Summer School

Differences between Fisher’s Exact Test and GSEA for Functional Enrichment

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

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