BigBio Stack

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49 repositories

pmultiqc
Public
A library for QC report based on MultiQC framework
Python
•
MIT License
•16•21•3•1•Updated Sep 30, 2025Sep 30, 2025
quantms.io
Public
The proteomics quantification format, extending mzTab for large scale datasets.
Python
•
Other
•6•12•26•1•Updated Sep 30, 2025Sep 30, 2025
sdrf-pipelines
Public
`sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files
proteomics mass-spectrometry openms maxquant msstats multiomics sdrf proteomics-data-analysis
Python
•
Apache License 2.0
•26•21•33•1•Updated Sep 27, 2025Sep 27, 2025
ibaqpy
Public
Absolute quantification package based on quantms.io
proteomics mass-spectrometry quantification absolute-quantification ibaq
HTML
•
MIT License
•13•16•2•0•Updated Sep 25, 2025Sep 25, 2025
quantms-readthedocs
Public
This repository contains the documentation of quantms workflow
Batchfile
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MIT License
•0•0•0•0•Updated Sep 24, 2025Sep 24, 2025
proteomics-sample-metadata
Public
The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
metadata proteomics proteomics-datasets multiomics proteomexchange sdrf pride-metadata msrun-metadata sdrf-proteomics proteomics-community
GNU General Public License v2.0
•112•96•75•4•Updated Sep 22, 2025Sep 22, 2025
quantms
Public
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
proteomics mass-spectrometry proteogenomics tmt lfq
Nextflow
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MIT License
•48•57•59•0•Updated Sep 15, 2025Sep 15, 2025
hvantk
Public
Hail variant annotation toolkit
big-data genomics bigdata hail variant-analysis
Python
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MIT License
•0•0•5•0•Updated Sep 11, 2025Sep 11, 2025
onsite
Public
onsite: posttranslation modification site localization
Python
•
MIT License
•1•0•1•0•Updated Aug 27, 2025Aug 27, 2025
quantms-test-datasets
Public
Python
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MIT License
•0•0•0•0•Updated Aug 16, 2025Aug 16, 2025
quantms-rescoring-paper
Public
TeX
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Creative Commons Zero v1.0 Universal
•6•1•2•1•Updated Aug 13, 2025Aug 13, 2025
quantms-rescoring
Public
quantms and ms2rescore helper functions and scripts
Python
•
Apache License 2.0
•1•0•0•0•Updated Aug 12, 2025Aug 12, 2025
quantms-containers
Public
DIANN docker container and OpenMS release for quantms
Dockerfile
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Apache License 2.0
•2•2•0•0•Updated Jul 17, 2025Jul 17, 2025
SDRFscribe
Public
AI assistant of SDRF annotations.
Apache License 2.0
•1•0•0•0•Updated Jul 11, 2025Jul 11, 2025
DLEAMSE
Public
A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring
Python
•
Apache License 2.0
•4•11•3•1•Updated Jun 18, 2025Jun 18, 2025
quantms.org
Public
Web page storing all the datasets renalyzed with quantms
Vue
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MIT License
•4•0•0•0•Updated Jun 2, 2025Jun 2, 2025
quantms-utils
Public
A python library with scripts and helpers classes for quantms workflow
cloud nextflow bigdata proteomics mass-spectrometry proteogenomics
Python
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MIT License
•4•5•0•0•Updated May 14, 2025May 14, 2025
.github
Public
MIT License
•0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
sdrf-cellline-metadata-db
Public
SDRF Cell Line Metadata Database
metadata annotations proteomics mass-spectrometry hupo-psi sdrf sdrf-proteomics celllines
Python
•
Apache License 2.0
•0•0•0•0•Updated Jan 20, 2025Jan 20, 2025
sdrf-utils
Public
sdrf-cls
Python
•
Apache License 2.0
•1•0•0•0•Updated Dec 18, 2024Dec 18, 2024
spectrafuse
Public
Incremental clustesting pipeline from quantms data.
Python
•
MIT License
•0•1•4•0•Updated Nov 18, 2024Nov 18, 2024
pgatk-io
Public archive
High performance io library for proteogenomics
spark parquet proteomics mass-spectrometry proteogenomics fileformats
Java
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Apache License 2.0
•0•1•1•1•Updated Oct 8, 2024Oct 8, 2024
fslite
Public
Lightweight Feature selection Python library
scikit-learn feature-selection multiomics
Python
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Apache License 2.0
•1•1•4•1•Updated Sep 26, 2024Sep 26, 2024
pyspectrafuse
Public
Python library with utility scripts for spectrafuse pipeline
Python
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Apache License 2.0
•1•0•0•1•Updated Jun 26, 2024Jun 26, 2024
pgt-pangenome
Public
Protegenomics analysis based on Pangenome references
protein variants proteomics mass-spectrometry pangenome proteogenomics non-canonical quantms public-proteomics
Jupyter Notebook
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BSD 2-Clause "Simplified" License
•0•1•0•0•Updated May 25, 2024May 25, 2024
py-pgatk
Public
Python tools for proteogenomics analysis toolkit
python vcf ensembl proteomics mass-spectrometry proteogenomics proteogenomics-analysis-toolkit
Python
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Apache License 2.0
•12•13•9•0•Updated Apr 26, 2024Apr 26, 2024
msgfplus
Public
MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
search-engine proteomics mass-spectrometry sequential-algorithm
Java
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Other
•37•0•1•0•Updated Mar 26, 2024Mar 26, 2024
mad_decoy
Public
Mad decoy is a decoy simulation tool to assess large-scale merge of q-values.
Python
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Apache License 2.0
•2•0•0•0•Updated Nov 4, 2023Nov 4, 2023
tdf2mzml
Public
quantms bruker to mzml
Python
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Other
•17•0•0•0•Updated Oct 2, 2023Oct 2, 2023
qccalculator
Public
Development for python driven QC calculation (QCCalculator)
HTML
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Apache License 2.0
•1•3•0•0•Updated Nov 30, 2022Nov 30, 2022