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Cellxgene Census Explorer

cellxgene-census

K-Dense-AI/claude-scientific-skills

Provides programmatic access to the CZ CELLxGENE Census (61M+ cells) for querying standardized single-cell expression, metadata, embeddings, and stats across tissues and diseases, supporting scanpy and ML workflows.

COSMIC Mutation Access

cosmic-database

K-Dense-AI/claude-scientific-skills

Programmatic access to the COSMIC cancer mutation database for downloading mutations, Cancer Gene Census, mutational signatures, fusions, copy number, expression, and resistance data to fuel oncology research or bioinformatics pipelines after authentication.

GEO Data Retriever

K-Dense-AI/claude-scientific-skills

Connect to NCBI's GEO repository, search series/samples/platforms via Entrez queries, fetch profiles, and download raw/processed matrices using GEOparse for transcriptomics and expression analysis workflows.

PyDESeq2 Differential Analysis

K-Dense-AI/claude-scientific-skills

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

Reactome Pathway Explorer

reactome-database

K-Dense-AI/claude-scientific-skills

Query the Reactome Content and Analysis Services (or the reactome2py client) to fetch pathway hierarchies, map genes, run overrepresentation/expression analyses, and explore disease interactions for systems biology research.

Single-Cell Generative Toolkit

K-Dense-AI/claude-scientific-skills

Probabilistic deep-learning framework built on PyTorch for single-cell omics; handles batch correction, integration, multimodal and spatial data, differential expression, and transfer learning with unified APIs.

cBioPortal Cancer Data

cbioportal-database

K-Dense-AI/claude-scientific-skills

Access multi-dimensional cancer genomics data via cBioPortal REST API for mutation, copy-number, expression, and survival insights across TCGA/GENIE studies, enabling target validation and clinical association analyses programmatically with Python clients.

GTEx Expression Explorer

K-Dense-AI/claude-scientific-skills

Query the GTEx portal and API to retrieve tissue-specific gene expression, eQTL, sQTL, and variant-level regulatory data for interpreting GWAS loci and exploring gene regulation across 54 human tissues.

Cellxgene Census Explorer

cellxgene-census

K-Dense-AI/scientific-agent-skills

Provides programmatic access to the CZ CELLxGENE Census (61M+ cells) for querying standardized single-cell expression, metadata, embeddings, and stats across tissues and diseases, supporting scanpy and ML workflows.

PyDESeq2 Differential Analysis

K-Dense-AI/scientific-agent-skills

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

Single-Cell Generative Toolkit

K-Dense-AI/scientific-agent-skills

Probabilistic deep-learning framework built on PyTorch for single-cell omics; handles batch correction, integration, multimodal and spatial data, differential expression, and transfer learning with unified APIs.

Arbitrary Precision Math Calculator

Code-and-Sorts/awesome-copilot-agents

This utility evaluates complex arithmetic expressions using arbitrary-precision decimal mathematics. It is specifically designed for scientific, financial, or engineering calculations where standard floating-point arithmetic causes unacceptable rounding errors (e.g., 0.1 + 0.2). Supports addition, subtraction, multiplication, division, exponents, and parentheses.

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