BigBio Stack
- 65 followers
- Cambridge, UK
- ypriverol@gmail.com
bigbio is an open-source organization dedicated to advancing bioinformatics and computational proteomics and multiomics research. We develop scalable tools, workflows, and libraries to support complex experimental designs in proteomics, genomics and multiomics. Our mission is to empower researchers with accessible, efficient, and cutting-edge solutions for data analysis and integration.
- quantms: A comprehensive workflow for proteomics experiments supporting DDA-LFQ, DDA-Isobaric, and DIA-LFQ quantification.
- qpx: A proteomics quantification format extending mzTab for large-scale datasets.
- ibaqpy: A package for absolute quantification based on the quantms.io format.
- quantms.org: Code for quantms.org, a resource for reanalysis and public proteomics data.
- multiomics-configs: Config files for species, taxonomies, and other essential data.
- proteomics-sample-metadata: A standard for experimental design annotation in proteomics datasets.
- sdrf-pipelines: Tools to convert SDRF proteomics files into pipeline configuration files.
- pmultiqc: A QC report library based on the MultiQC framework.
- spectrafuse: An incremental clustering pipeline for quantms data.
- quantms-utils: Helper scripts and classes for the quantms workflow.
- quantms-rescoring: Helper functions and scripts for quantms and ms2rescore.
We welcome contributions from the community! Whether it's bug fixes, feature suggestions, or documentation improvements, every contribution helps drive bioinformatics research forward.
- Website: quantms.org
- GitHub: bigbio GitHub
Join us on this journey to revolutionize data analysis in proteomics and beyond!
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Repositories
- andes Public
- sdrf-annotated-datasets Public
A repository of datasets in ProteomeXchange annotated in SDRF, previously part of the specification
- mokume Public
Integrated library to perform feature normalization and multiple abundance computing based on qpx
- proteomics-sample-metadata Public
SDRF: The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
- sdrf-templates Public
SDRF templates and validation yaml files from specification proteomics-sample-metadata
- quantms Public
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
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