English | 中文
I build pipelines and analyze grapevine genomes, focusing on clones, pangenomes, transposable elements, capture panels, ancient DNA, and population genetics theory.
ORCID 0000-0003-3670-6657 | paper-viz gallery | grapeancestry demo
Run 123 R figure templates to generate vector PDFs and 600 dpi PNGs. |
Map new grapevine samples to a frozen 2449 × 167K panel and build interactive HTML reports. |
Turn a local research PDF into a Chinese illustrated L3 note; your PDF library stays on your machine. |
Run workflows for Vitis pangenome graphs, presence/absence variation, and mixed-variant dosage. |
Sort ADMIXTURE Q files, align columns across K, and draw structure barplots. |
Mine classic genomics theories and test their assumptions on modern grapevine clones and wild Vitis. |
| Repository | What it does |
|---|---|
| vitis-pangenome | Scripts and workflows for Vitis pangenome graphs, presence/absence variation, and mixed-variant/dosage methods. |
| gene-structure-annotation | Pipelines for structural genome annotation, providing gene models and GFF3 outputs from FASTA and evidence. |
| gene-function-annotation | Assigns functional labels like GO, KEGG, and domains to protein sequences after structure annotation. |
| grapevine-plastid · In progress | Vitis plastid / chloroplast pangenome notes |
| vitis-te · In progress | Public stub for Vitis TE libraries and the soft-mask hand-off into gene annotation pipelines. |
| Repository | What it does |
|---|---|
| grapeancestry | 167K grapevine capture panel companion: ancestry, identity, PCA, colour GS. |
| gtbs-chip-service-kit | Register an existing genotyping chip as a profile and check it. |
| grapevine-chip | Grapevine capture-array / 167K chip design |
| Repository | What it does |
|---|---|
| qbar | Sort ADMIXTURE Q files, align columns across K, and draw structure barplots. |
| TrioConcordance | Python tool for locus-by-locus and sample-by-sample genotype concordance analysis across three independent datasets. |
| genomics-theory-mining | Mine a classic genomics theory and test it on modern data. |
| vitis-popgen · In progress | Vitis population genetics and domestication |
| Repository | What it does |
|---|---|
| grapevine-adna · In progress | Ancient-DNA methods and notes for Vitis |
| Repository | What it does |
|---|---|
| paper-viz | R-first publication figure gallery: 123 templates plus 21 schematics (code + simulated data + preview), browsable web gallery, agent-callable. |
| paper-reading | Turns one research PDF into a Chinese illustrated reading note; your PDF library stays on your machine. |
| literature-review-skills | An agent-agnostic skill suite for writing literature reviews that stops at human gates, with every claim tied to a source the project actually holds. |
| patent-drafting-skills | Bilingual (EN/中文) agent skills for drafting invention patents — CN, US and PCT: disclosure, prior-art search, inventive step, claims, description, drawings, consistency checks, .docx export. |
| concept-learning | Homemade Cursor skill: biology concept lessons and BioLogos-style series writing. |
| famous-people | Homemade Cursor skill: one biologist's scientific life as a Chinese WeChat longread. |
| awesome-astra-science | AI model works: demos and figures the models actually produced. |
| cursor-state-vscdb | Scripts and case study for diagnosing macOS Cursor hangs caused by tens-of-GB state.vscdb SQLite databases. |
| grok-bot-dispatch | Cursor skill: Primary is the front door. Project bots stay in Unassigned. A role is a one-task assignment on a shared pool. |
| Topic | Repositories |
|---|---|
| Grapevine genome | vitis-te (soft-masking stub), grapevine-plastid (methods to come) |
| Genome annotation | gene-structure-annotation (gene models: GFF3 + proteins), gene-function-annotation |
| Target-sequencing genotyping | gtbs-chip-service-kit (validates chip profiles; steps documented in steps/), grapevine-chip (design notes) |
| Population genetics | vitis-popgen (placeholder), TrioConcordance |
| Ancient DNA | grapevine-adna (placeholder) |