bio-proteomics-ptm-analysis
PKU-YuanGroup/OpenAI4SFrames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and…
Scores out of 100 · grade A
2026-08-22Works
40% of the score100/100
- Loads cleanly: valid frontmatter, required fields present, no dangling references.
Maintained
25% of the score100/100
- no commits in the last 12 weeks
Adopted
20% of the score35/100
- 335 stars on the source repo.
Documented
15% of the score100/100
- 3,578 words with worked examples.
- Ships 2 bundled files.
Install
npx skills add PKU-YuanGroup/OpenAI4S/bio-proteomics-ptm-analysisWhat it says it does
Frames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and protein-level-adjusted quantification with MSstatsPTM - plus kinase-activity and functional triage. Covers MaxQuant Phospho (STY)Sites multiplicity expansion, localization-probability filtering (class I, Ascore, ptmRS, DIA EG.PTMLocalizationProbabilities, DIA-NN PTM.Site.Confidence), false localization rate (LuciPHOr/DeepFLR), motif analysis with experiment-matched backgrounds, diGly/K-GG ubiquitin specificity, acetyl/glyco traps, and KSEA/PTM-SEA. Use when localizing and quantifying phosphorylation, acetylation, ubiquitination, or glycosylation sites from enrichment-based runs and deciding whether an apparent site change is real after subtracting protein abundance. Peptide ID and open/variable-mod search is peptide-identification; underlying protein-level quant is quantification and differential-abundance; DIA acquisition mechanics is dia-analysis.
Also in PKU-YuanGroup/OpenAI4S
| Artifact | Score | What the check found | Type | Reach | Last commit |
|---|---|---|---|---|---|
| bio-atac-seq-allele-specific-accessibilityPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-atac-peak-callingPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-consensus-peaksetPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-deep-learning-atacPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-footprintingPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-causal-genomics-effector-gene-prioritizationPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today |
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