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 by simultaneously leveraging multiple references, enabling cross-species annotation, and offering continuous updates without requiring researchers to curate their references. This approach simplifies single-cell data annotation, addressing key challenges like reference selection while ensuring high accuracy.
To learn more about this new feature, attend our webinar on February 13 with Dr. Ashwini Patel and Marta Benegas, “ Advanced Multi-Reference Cell Type Prediction with CellKb in OmicsBox”
Dr. Stefan Götz, CEO of BioBam, commented:
“The OmicsBox version we are presenting this year in San Diego introduces significant advancements in single-cell and long-read transcriptomics and expanded microbiome analysis capabilities. With these developments, we aim to support our users in addressing these challenging research areas.”
OmicsBox 3.4 also introduces major improvements, including a taxonomic classification for metagenomics using Silva, Greengenes, and GTDB databases, a redesigned PacBio IsoSeq pipeline, and new tools for combining transcriptomes with TAMA Merge in long-read transcriptomics.
Below is a detailed list of the new features and improvements included in this release:
Functional Analysis
- New Kegg and Reactome Pathway Browser
- Improved Combined Pathway Viewer with Sticky Tooltips
- Improved Pathway Export Options via Context Menu and Side Panel
- Improved Options for the ORF Finder Tool
- Update of Diamond Blast DataBase
Metagenomics
- New PCoA Configuration Options
- New Kraken Databases: UNITE Fungi and MiDAS 5
- Update of Kraken RefSeq Database
Transcriptomics
- New Experimental Design Export Option for Differential Expression Results
General
- Fixed Display Scaling Issue in Windows 10/11
- Fixed Issue with Dark Mode in the MacOS
About OmicsBox:
OmicsBox is a leading bioinformatics software platform designed for end-to-end analysis of genomes, transcriptomes, and metagenomes. This user-friendly desktop application is efficient and powerful, enabling researchers to uncover valuable biological insights from complex omics data.
Trusted by top private and public research institutions worldwide, OmicsBox simplifies the processing of large datasets, streamlining the analysis workflow. Its modular structure provides tailored tools and functions for diverse analyses, including de novo genome assembly, genetic variation analysis, differential expression analysis, and taxonomic classification of microbiome data. OmicsBox also supports functional interpretation and offers rich data visualization capabilities.
The functional analysis module, featuring the renowned Blast2GO annotation methodology, is particularly well-suited for non-model organism research—a fact supported by over 15,000 scientific citations.
Try OmicsBox 3.4 for free now! Download our Free Trial here. OmicsBox is compatible with standard PCs and laptops running Windows, Linux, or Mac, offering a seamless experience right out of the box.
