Owner
bigbio
19 indexed repositories · View on GitHub
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proteomics-sample-metadata
SDRF: The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
HTML · 116 stars
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quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Iso...
Nextflow · 83 stars
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sdrf-pipelines
SDRF official validator and converts SDRF to pipeline configuration files
Python · 37 stars
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pmultiqc
A library for QC report based on MultiQC framework
Python · 34 stars
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qpx
qpx (Quantitative Proteomics eXchange) format (aka quantms.io) a format to capture a full proteomics experiment
Python · 26 stars
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quantmsdiann
quantms workflow for DIANN tool including DIA and DDA analysis
Nextflow · 19 stars
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sdrf-skills
Agentic plugins to annotate SDRF using Claude; Codex; Cursor; Gemini
Python · 18 stars
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pgatk
Python tools for proteogenomics analysis toolkit
Python · 17 stars
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ibaqpy
Absolute quantification package based on quantms.io
HTML · 16 stars
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sdrf-templates
SDRF templates and validation yaml files from specification proteomics-sample-metadata
Python · 5 stars
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pepgenome
Proteogenomics tool that enables to map peptides to genome coordinates
Java · 4 stars
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onsite
onsite: posttranslation modification site localization
Python · 4 stars
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rawQC
This library enables to compute idfree QC metrics for mzML files using pyopenms
Jupyter Notebook · 3 stars
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fslite
Lightweight Feature selection Python library
Python · 2 stars
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Rust · 2 stars
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spectrafuse
Incremental clustesting pipeline from quantms data.
Nextflow · 1 star
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hvantk
Hail variant annotation toolkit
Python · 1 star
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quantms-portal
Tooling and frontend for portal.quantms.org — AI-first proteomics data portal
Vue · 1 star
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relink
A nextflow workflow for the analysis of large-scale crosslinking experiments
Nextflow · 0 stars
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bigbio/pepgenome#2 · 2 comments · 0 reactions · 0 assignees ·
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bigbio/pepgenome#1 · 12 comments · 0 reactions · 0 assignees ·
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bigbio/ibaqpy#104 · 5 comments · 0 reactions · 0 assignees ·
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bigbio/ibaqpy#107 · 0 comments · 0 reactions · 0 assignees ·
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bigbio/ibaqpy#108 · 0 comments · 0 reactions · 0 assignees ·
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documentation enhancement good first issue
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documentation
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benchmarking
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documentation
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documentation enhancement good first issue
bigbio/spectrafuse#4 · 0 comments · 0 reactions · 1 assignee ·
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bigbio/spectrafuse#6 · 0 comments · 0 reactions · 0 assignees ·
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extend support Open
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bigbio/sdrf-skills#68 · 1 comment · 0 reactions · 0 assignees ·
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bigbio/sdrf-skills#69 · 1 comment · 0 reactions · 0 assignees ·
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massive-files is broken: MassIVE FTP now requires TLS, and the failure is reported as a timeout Open
bigbio/sdrf-skills#72 · 0 comments · 0 reactions · 0 assignees ·
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bigbio/sdrf-skills#73 · 0 comments · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#184 · 1 comment · 0 reactions · 2 assignees ·
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Versioning scheme Open
bigbio/sdrf-pipelines#213 · 0 comments · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#214 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
bigbio/sdrf-pipelines#232 · 0 comments · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#238 · 1 comment · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#239 · 1 comment · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#245 · 0 comments · 0 reactions · 1 assignee ·
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low-priority
bigbio/sdrf-pipelines#258 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
bigbio/sdrf-pipelines#271 · 0 comments · 0 reactions · 1 assignee ·
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bigbio/sdrf-pipelines#283 · 0 comments · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#333 · 0 comments · 1 reaction · 2 assignees ·
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Bundled ontology cache is stale: PRIDE:0001013 (study sample) missing, fails --use_ols_cache_only Open
bigbio/sdrf-pipelines#341 · 0 comments · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#344 · 1 comment · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#345 · 0 comments · 0 reactions · 0 assignees ·
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bigbio/sdrf-pipelines#346 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
bigbio/quantms#69 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
bigbio/quantms#79 · 0 comments · 0 reactions · 0 assignees ·
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enhancement question
bigbio/quantms#273 · 5 comments · 0 reactions · 0 assignees ·
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enhancement help wanted high-priority
bigbio/quantms#283 · 0 comments · 0 reactions · 0 assignees ·
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bug
bigbio/quantms#299 · 1 comment · 0 reactions · 3 assignees ·
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enhancement help wanted high-priority
bigbio/quantms#303 · 8 comments · 0 reactions · 1 assignee ·
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bug
bigbio/quantms#327 · 13 comments · 0 reactions · 1 assignee ·
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bug
bigbio/quantms#329 · 11 comments · 0 reactions · 3 assignees ·
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bug enhancement high-priority
bigbio/quantms#340 · 2 comments · 0 reactions · 2 assignees ·
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documentation enhancement high-priority
bigbio/quantms#344 · 4 comments · 0 reactions · 2 assignees ·
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documentation enhancement high-priority open-search sage-support
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bug
bigbio/quantms#364 · 3 comments · 0 reactions · 4 assignees ·
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enhancement high-priority research-projects
bigbio/quantms#410 · 13 comments · 0 reactions · 3 assignees ·
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enhancement
bigbio/quantms#411 · 12 comments · 0 reactions · 0 assignees ·
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enhancement
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enhancement high-priority
bigbio/quantms#434 · 0 comments · 0 reactions · 3 assignees ·
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enhancement question
bigbio/quantms#440 · 8 comments · 0 reactions · 4 assignees ·
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enhancement
bigbio/quantms#455 · 20 comments · 0 reactions · 3 assignees ·