Skill Claude CodeCodex
Core skills for single-cell RNA-seq analysis: quality control, cell type annotation, and trajectory inference. These are high-priority actionable workflows — load them first for common single-cell tasks.
Skill Claude CodeCodex
Skills for spatial transcriptomics analysis including single-cell to spatial mapping (MOSCOT), 3D visualization (PyVista), and related spatial workflows.
Skill Claude CodeCodex
Skills for upstream data processing in single-cell and spatial omics, covering raw data generation, barcode processing, alignment, spatial registration, and technology-specific preprocessing pipelines.
Skill Claude CodeCodex
Skills for using nf-core community pipelines to process omics data, from installation and configuration to running specific analysis pipelines.
Skill Claude CodeCodex
Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.
Skill Claude CodeCodex
Routing and workflow skill family for paper-writing tasks. Covers manuscript drafting, journal and conference papers, grant proposals, lab reports, group-meeting reports, talks, workshop notes, reviewer rebuttals, academic HTML/PDF/LaTeX output with editable-block contracts, citation grounding, evidence checking, and…
Skill Claude CodeCodex
Scenario router for paper-writing tasks. Use after root triage to select paper submission, journal article, conference paper, grant proposal, lab report, group report, talk/workshop, or revision-response behavior.
Skill Claude CodeCodex
Workflow phases for paper-writing tasks: triage, material inventory, research question, literature review, paper outline, data analysis summary, figure storyline, reader testing, and finalize packet. Each phase is a short contract — read the relevant rows for the current task only.
Skill Claude CodeCodex
Section-level writing skill for evidence-bound academic prose: IMRaD papers, grants, reports, talks, and response letters. Indexes section-specific templates (abstract, introduction, method, results, discussion) and pre-submission quality protocols (claim-evidence, reviewer rubric, response letter).
Skill Claude CodeCodex
Skills for creating presentations, slides, and visual documentation.
Skill Claude CodeCodex
Skills for rare disease case support: ontology-first normalization/retrieval and the clinical genetics consult report format contract (structure + theme). Load the relevant skill file when performing the matching task.
Skill Claude CodeCodex
Obtain and predict protein 3D structures — fetch AlphaFold predicted models from the AlphaFold DB, experimental structures from the RCSB PDB, or predict a novel sequence with ColabFold — and visualise them in the Mol desktop app.
Skill Claude CodeCodex
Query the Virtual Embryo knowledge graph (mouse/human developmental biology: genes, anatomy, Theiler/Carnegie stages, gene expression, diseases, papers) and its 3D atlas catalog (anatomical OPT/light-sheet volumes + 3D spatial- transcriptomics datasets), and visualise those datasets in 3D with the volume3d / spatial3d…
aristoteleo/awesome-skill-generate
Skill Claude CodeCodex
Run or adapt dynamo preprocessing with dynamo.preprocessing.Preprocessor, including the recipe branches monocle, seurat, sctransform, pearsonresiduals, and monoclepearsonresiduals. Use when converting or reproducing docs/tutorials/notebooks/100tutorialpreprocess.ipynb, preprocessing an AnnData object for downstream…
aristoteleo/awesome-skill-generate
Skill Claude CodeCodex
Create or update a Codex skill that packages reusable workflows, references, scripts, and assets for repeated tasks. Use when turning notebooks, tutorials, analyses, or domain procedures into a triggerable local skill for other agents, or when deciding whether a notebook subset or branch should update an existing…
aristoteleo/awesome-skill-generate
Skill Claude CodeCodex
Evaluate the quality of a Codex skill from multiple dimensions and produce a structured score, verdict, and revision guidance. Use when reviewing a SKILL.md, scoring a skill folder, comparing two skills, performing cross-review on a newly created skill, or checking whether a skill is triggerable, executable, concise…