Skills
All skills are lab-validated fixed scripts packaged in the standard SKILL.md format. Chinese tutorials are online; English tutorials are being prepared.
🧪 Experiment Data Processing
| Skill | What it does |
|---|---|
| qPCR mRNA (ΔΔCt) | Relative expression from raw Ct tables, one plot per target |
| qPCR mtDNA copy number | ND1/ND5 + B2M/POLG pairing, mean copy number |
🧬 Bioinformatics Analysis
| Skill | What it does |
|---|---|
| Single-cell RNA-seq | Raw matrices → QC → Harmony → clustering → UMAP → markers → SingleR annotation |
| scRNA-seq pseudotime | monocle3 trajectory on the regular pipeline's annotated rds |
| scRNA-seq virtual KO | scTenifoldKnk in-silico gene knockout |
| Bulk RNA-seq DEG | Counts → QC → DEG, auto engine fork (limma-trend / DESeq2 / edgeR+voom) |
| Enrichment (GO/KEGG/Reactome) | GO/Reactome offline, KEGG online + cache fallback |
| Gene expression plots | One gene across groups / two genes within group |
| GSEA | fgsea + MSigDB GMT, auto Entrez/symbol conversion |
| Phylo tree — build | Genome FASTAs → bcgTree → IQ-TREE2 treefile (WSL2) |
| Phylo tree — plot | Treefile + annotation CSV → publication-ready ggtree figure |
📈 Figure & Table Generation
| Skill | What it does |
|---|---|
| Grouped bar plot | Wide-format CSV → 300-dpi annotated bar plot |
| Clinical tables | One pipeline reproducing all 10 tables of a paper: baseline / Firth / genotype cross-tabs / univariate |
| Survival curve | Optimal-cutoff KM curve + risk table + Cox forest plot |