CHENyiru3

CHENyiru3/AI-Skills-Collections

Skill Codex

Review computational biology algorithm-development projects and consolidate past experiments into an evidence-linked Markdown experience report. Use for experiment retrospectives, learning from biological or technical failures, and recovering reusable lessons from mixed project folders. Start from the project index or…

CHENyiru3/AI-Skills-Collections

Skill Claude Code

Acts as a peer review assistant to evaluate bioinformatics manuscripts. Identifies missing baselines, methodological flaws, and data leakage.

CHENyiru3/AI-Skills-Collections

Skill Claude Code

Drafts highly precise Methods sections for spatial transcriptomics, single-cell RNA-seq (e.g., muscle aging/regeneration), and 3D interpolation pipelines.

CHENyiru3/AI-Skills-Collections

Skill Claude Code

Translates complex deep learning architectures (VQ-VAE, Transformers, Neural ODEs) into standard biological manuscript text, focusing on the biological rationale for the architecture.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Multi-omics integration for single-cell data. Use for integrating multiple modalities like RNA, ATAC, and protein in single-cell analysis.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

R package for single-cell ATAC-seq analysis. Use for chromatin accessibility analysis, peak calling, motif enrichment, and integration with gene expression.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

R package for chromatin analysis. Use for single-cell ATAC-seq analysis, chromatin accessibility, and integration with Seurat.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Convert between .h5ad (AnnData) files and R single-cell data formats (Seurat, SingleCellExperiment) using anndataR. Use this skill whenever the user mentions: h5ad files, AnnData objects, converting between Python scanpy and R (Seurat/SingleCellExperiment), moving single-cell data between Python and R ecosystems, or…

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

R package for single-cell trajectory analysis. Use for reconstructing pseudotime trajectories, identifying cell differentiation paths, analyzing branch points, and ordering cells along developmental processes. Best for understanding dynamic biological processes from scRNA-seq data.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use…

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

R package for converting h5ad files (HDF5 AnnData format from scanpy) to Seurat or SingleCellExperiment objects. Use whenever working with single-cell data in h5ad format that needs to be converted to R. Includes support for Visium spatial transcriptomics data, raw counts, cell metadata, and dimensionality reduction…

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

R package for single-cell RNA-seq analysis. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and multi-modal integration. Best for R-based single-cell workflows. For Python use scanpy.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Batch-balanced k-nearest neighbors for single-cell data integration. Fast and simple Python implementation for batch correction.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Fast and accurate integration of single-cell data. Use for batch correction and data integration. Works with Seurat objects in R. For Python use scanorama or bbknn.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Python package for single-cell data integration. Use for batch correction and integrating multiple single-cell datasets. Fast and accurate.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

R package for multi-modal single-cell data integration (v5). Use for analyzing CITE-seq, ADT, and other multi-modal single-cell data. For Python use scanpy with multi-omics.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Interactive web-based viewer for single-cell RNA-seq data. Use for exploring datasets, creating visualizations, and sharing results. For programmatic access use cellxgene-census.

CHENyiru3/AI-Skills-Collections

Skill Claude CodeCodex

Toolkit for spatial genomics. Comprehensive R package for spatial transcriptomics analysis with advanced visualization and statistics.