𧬠Plant genomics | π Vitis | β³ Ancient DNA
Grapevine genetics: clones, pangenomes, transposable elements, capture arrays, and tests of old population-genetic theory on modern data.
Annotation teaching pair (structure β function; TE library build is a separate job under Lines of work):
- π·οΈ gene-structure-annotation β primary gene-model layer (exons / CDS β GFF3 + proteins; TE soft-mask inside structure)
- π·οΈ gene-function-annotation β labels after proteins (GO / domains / names; no BRAKER / GFF edit / TE)
Annotation board: Project #2 (structure β function).
Grapevine tool:
- π grapeancestry β grapevine 167K public walkthrough (GUIDELINE /
demo//steps/); reusable chip scaffold is gtbs-chip-service-kit
- π§° gtbs-chip-service-kit β GBTS Chip Service Kit (generic scaffold)
- π grapeancestry β grapevine 167K walkthrough (
demo//steps/); chip scaffold β kit above - 𧬠grapevine-adna β ancient DNA
- πΈοΈ vitis-pangenome β pangenome / graph
- 𧱠vitis-te β transposable elements
- π vitis-popgen β population genetics
- π’ grapevine-plastid β plastid
- π§° bioinfo-agent-skills β public index (each skill is its own repo)
- π genomics-theory-mining β one theory per folder; original paper first
β οΈ bioinfo-pitfalls β symptom-first traps for plant genomics pipelines- π vitis-synteny β colinearity / synteny
- π·οΈ gene-structure-annotation β gene structure / models (ex plant-gene-annotation)
- π·οΈ gene-function-annotation β gene functional annotation (ex vitis-gene-annotation)
- π plant-lit-review β literature review workflow
- ποΈ plant-omics-db β plant multi-omics databases
- π€ famous-people β one person, one checkable question
- π± concept-learning β biology / evolution concept lessons
- π paper-reading β one PDF to one Chinese L3 note
- πΌοΈ paper-viz β featured R-first paper-figure library (116 templates: simulated data + code + preview). Repo: https://github.com/Xuzhen-Li/paper-viz Β· Gallery: https://xuzhen-li.github.io/paper-viz/
- πΌοΈ awesome-astra-science β Astra science gallery (wins + δΉε°±ι£εδΊ)
- β TrioConcordance β trio genotype QC
- π§― cursor-state-vscdb β Cursor stuck on Loading chats: oversized
state.vscdb/cursorDiskKVcase write-up
- Old theory, new data β lock the original paper, list the assumptions, then try to break them on grape clones and wild Vitis
- Capture panel β GBTS kit scaffold (
gtbs-chip-service-kit) + grapevine 167K walkthrough (grapeancestry) - Clonal genomes β aDNA, pangenomes, TE, and plastid as separate jobs, not one dump
VitisGDB is my grapevine database work. The public GitHub copy is currently published with a collaborator.
Read the original. Name the assumption that dies in clones. One theory per folder.