A general, evolvable, and distributed agent framework & harness for data science.
Skill Claude CodeCodex
This directory contains bioinformatics upstream analysis skills for agent-assisted data processing. Each skill provides workflow guidance, code templates, and best practices for specific analysis types.
Skill Claude CodeCodex
Here are some skills about the best practices for analyzing the single-cell/Spatial Omics data. When you need to do the specific analysis tasks described in this file, you can load the related skill files linked here to help you.
Skill Claude CodeCodex
Skills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.
Skill Claude CodeCodex
Cell and nucleus segmentation tools for microscopy images. Covers Cellpose, SAM-based methods, StarDist, InstanSeg, and Mesmer.
Skill Claude CodeCodex
Drive the user's Atrium desktop: open files in installed viewer apps (Viv bioimages, Vitessce/Spatial 3D omics, Mol structures, IGV/Gosling genomics, Volume 3D, Cytoscape, MSA, PhyloTree, RDKit), read and steer ANY window — including ones the user opened — and call app backends.
Skill Claude CodeCodex
Aesthetic guidelines and output-type recipes for scientific figure production. Supports lightweight default-agent use through SKILL.md + one outputType recipe, with optional venue-specific style guides when requested.
Skill Claude CodeCodex
Skills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.
Skill Claude CodeCodex
Skills for querying and downloading data from genomic, transcriptomic, 3D-genome, and cancer-genomics databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, processed functional-genomics tracks, Hi-C / Micro-C contact matrices, TCGA-style cohorts, and large-scale single-cell…
Skill Claude CodeCodex
Panel design for DEVELOPING / dynamic systems (embryonic organs, differentiation, regeneration). The target experiment is usually a LATE / terminal stage, but the biology is a trajectory: terminal cell types are end-products of earlier lineage programs. A panel built from the target stage alone resolves terminal…
Skill Claude CodeCodex
End-to-end workflow for gene panel design in scRNA-seq and spatial transcriptomics, that should be STRICTLY followed: dataset understanding + smart downsampling + train/test splits, algorithmic selection (HVG/DE/RF/scGeneFit/SpaPROS), optimal sub-panel discovery (ARI vs size), biological completion with a stability…
Skill Claude CodeCodex
General-purpose skills for data analysis infrastructure: workspace file organization, environment management, parallel computing, and performance.
Skill Claude CodeCodex
Skills derived from the Single-cell Best Practices book (sc-best-practices.org). Comprehensive workflows and guidelines for single-cell and spatial omics analysis.
Skill Claude CodeCodex
Workflow guidance and model reference for single-cell foundation models (scGPT, Geneformer, UCE, scBERT, etc.). Covers model selection, validation-first workflow, and per-model I/O contracts.
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.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: