BigBio Stack

All

47 repositories

multiomics-configs
Public
Set of config files for species, taxonomies, etc
Shell
•2•3•79•0•Updated Jan 24, 2025Jan 24, 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
•
MIT License
•39•34•72•0•Updated Jan 23, 2025Jan 23, 2025
sdrf-pipelines
Public
A repository to convert SDRF proteomics files into pipelines config files
proteomics mass-spectrometry multiomics proteomics-data-analysis msstats sdrf
Python
•
Apache License 2.0
•23•16•26•1•Updated Jan 21, 2025Jan 21, 2025
sdrf-cellline-metadata-db
Public
SDRF Cell Line Metadata Database
metadata annotations proteomics mass-spectrometry hupo-psi sdrf sdrf-proteomics celllines
Python
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Apache License 2.0
•0•0•0•0•Updated Jan 20, 2025Jan 20, 2025
ibaqpy
Public
Absolute quantification package based on quantms.io
proteomics mass-spectrometry quantification absolute-quantification ibaq
Python
•
MIT License
•9•11•8•0•Updated Jan 16, 2025Jan 16, 2025
quantms.io
Public
The proteomics quantification format, extending mzTab for large scale datasets.
Python
•
Other
•4•7•18•0•Updated Jan 15, 2025Jan 15, 2025
quantms-rescoring
Public
quantms and ms2rescore helper functions and scripts
Python
•
Apache License 2.0
•1•0•0•0•Updated Jan 13, 2025Jan 13, 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 Jan 13, 2025Jan 13, 2025
quantms-utils
Public
A python library with scripts and helpers classes for quantms workflow
cloud nextflow bigdata proteomics mass-spectrometry proteogenomics
Python
•
MIT License
•1•5•0•0•Updated Dec 20, 2024Dec 20, 2024
sdrf-utils
Public
sdrf-cls
Python
•
Apache License 2.0
•1•0•0•0•Updated Dec 18, 2024Dec 18, 2024
diann-docker
Public
DIANN docker container based on the linux version from DIANN
Dockerfile
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Apache License 2.0
•0•0•0•0•Updated Nov 21, 2024Nov 21, 2024
spectrafuse
Public
Incremental clustesting pipeline from quantms data.
Python
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MIT License
•0•1•4•0•Updated Nov 18, 2024Nov 18, 2024
pmultiqc
Public
A library for QC report based on MultiQC framework
Python
•
GNU General Public License v3.0
•9•14•7•0•Updated Nov 10, 2024Nov 10, 2024
hvantk
Public
Hail variant annotation toolkit
big-data genomics bigdata hail variant-analysis
Python
•
MIT License
•0•0•1•0•Updated Nov 5, 2024Nov 5, 2024
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
•107•80•60•3•Updated Oct 16, 2024Oct 16, 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
•
Apache License 2.0
•1•1•4•1•Updated Sep 26, 2024Sep 26, 2024
DLEAMSE
Public
A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring
Python
•
Apache License 2.0
•4•11•3•0•Updated Jul 28, 2024Jul 28, 2024
pyspectrafuse
Public
Python library with utility scripts for spectrafuse pipeline
Python
•
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
•
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
•11•11•8•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
•36•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
•
Other
•14•0•0•0•Updated Oct 2, 2023Oct 2, 2023
openmsrescore
Public
OpenMS MSRescore tool, integration tool between MS2Rescore and OpenMS
Apache License 2.0
•0•0•0•0•Updated May 18, 2023May 18, 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
sage
Public
Proteomics searching so fast it feels like magic
Rust
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MIT License
•46•0•0•0•Updated Oct 13, 2022Oct 13, 2022
lucXor
Public
JAVA-based implementation of LuciPHOr that can process any variable PTM.
proteomics mass-spectrometry posttranslational-modification
Java
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Apache License 2.0
•8•0•2•0•Updated Sep 13, 2022Sep 13, 2022
pia
Public
📚 🔬 PIA - Protein Inference Algorithms
Java
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Other
•9•0•1•0•Updated Sep 8, 2022Sep 8, 2022
submission-tool-validator
Public
A command-line tool that provide functionalities to validate files that can be submitted to PRIDE
Java
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Apache License 2.0
•1•1•0•0•Updated Aug 26, 2022Aug 26, 2022