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Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,578 skills3 installs3,530 views
- Umap Learn--> --- name: bio-umap-learn description: UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Uniprot Database--> --- name: bio-uniprot-database description: 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. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Usfiscaldata--> --- name: bio-usfiscaldata description: Query the U.S. Treasury Fiscal Data API for federal financial data including national debt, government spending, revenue, interest rates, exchange rates, and savings bonds. Access 54 datasets and 182 data tables with no API key required. Use when working with U.S. federal fiscal data, national debt tracking (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates on Treasury securities...Votes: 0GitHub stars: 32
- Uspto Database--> --- name: bio-uspto-database description: Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Vaex--> --- name: bio-vaex description: Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that do not f...Votes: 0GitHub stars: 32
- Venue Templates--> --- name: bio-venue-templates description: Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requir...Votes: 0GitHub stars: 32
- What If Oracle--> --- name: bio-what-if-oracle description: Run structured What-If scenario analysis with multi-branch possibility exploration. Use this skill when the user asks speculative questions like "what if...", "what would happen if...", "what are the possibilities", "explore scenarios", "scenario analysis", "possibility space", "what could go wrong", "best case / worst case", "risk analysis", "contingency planning", "strategic options", or any question about uncertain futures. Also trigger when th...Votes: 0GitHub stars: 32
- Xlsx--> --- name: bio-xlsx description: "Use this skill any time a spreadsheet file is the primary input or output.\ \ This means any task where the user wants to: open, read, edit, or fix an existing\ \ .xlsx, .xlsm, .csv, or .tsv file (e.g., adding columns, computing formulas, formatting,\ \ charting, cleaning messy data); create a new spreadsheet from scratch or from\ \ other data sources; or convert between tabular file formats. Trigger especially\ \ when the user references a spreadsheet fil...Votes: 0GitHub stars: 32
- Zarr Python--> --- name: bio-zarr-python description: Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Zinc Database--> --- name: bio-zinc-database description: Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Charls Reproduce--> --- name: bio-charls-reproduce description: CHARLS (China Health and Retirement Longitudinal Study) database-specific knowledge for reproducing published papers. Use when reproducing or analyzing papers that use CHARLS data, including variable mapping from harmonized to raw questionnaire items, cognitive function scoring (episodic memory, mental status, TICS), CESD-10 depression screening, social isolation index construction, and chronic disease coding. Also use for any CHARLS data cleani...Votes: 0GitHub stars: 32
- Paper Reproduce--> --- name: bio-paper-reproduce description: 'Systematic methodology for reproducing published academic papers using provided data. Use when the user asks to reproduce, replicate, or verify results from a published paper, including sample selection, descriptive statistics, regression analyses, and generating reproduction reports (Markdown + LaTeX PDF). Covers the full pipeline: data exploration, variable identification/mapping, sample filtering, variable construction, statistical analysis, ...Votes: 0GitHub stars: 32
- Combined Database Lookup--> --- name: bio-combined-database-lookup description: Unified interface to query multiple biomedical databases (NCBI Entrez, Ensembl, UniProt, ChEMBL, PubChem) in a single workflow. tool_type: mixed primary_tool: Entrez measurable_outcome: Retrieve cross-referenced data from at least 3 databases for a single query within 60 seconds. allowed-tools: - run_shell_command - read_file --- Unified agent capability for cross-database exploration and data retrieval.Votes: 0GitHub stars: 32
- Source Management--> --- name: source-management description: Manages connected MCP sources for enterprise search. Detects available sources, guides users to connect new ones, handles source priority ordering, and manages rate limiting awareness. keywords: - sources - mcp - connections - priority - rate-limiting measurable_outcome: Accurately detects connected MCP tools and routes queries to appropriate sources based on query intent. allowed-tools: - read_file - run_shell_command --- > If you see unfamiliar p...Votes: 0GitHub stars: 32
- Biomed Dispatch--> --- name: bio-biomed-dispatch description: 'Dispatch biomedical research and data analysis tasks to Claude Code with K-Dense Scientific Skills. Use this skill when the user asks to run any bioinformatics, genomics, drug discovery, clinical data analysis, proteomics, multi-omics, medical imaging, or scientific computation task. Also use for literature search (PubMed, bioRxiv), pathway analysis, protein structure prediction, or scientific writing tasks. ' tool_type: mixed primary_tool: Unkn...Votes: 0GitHub stars: 32
- Paperzilla--> --- name: bio-paperzilla description: Reads content from URLs or files, classifies it, and generates structured summaries and comments in a specific, analytical style. Optimized for deep biomedical paper review. tool_type: mixed primary_tool: read_file measurable_outcome: Generate a structured analytical review of a biomedical paper with 100% citation accuracy. allowed-tools: - read_file - run_shell_command --- You are **Paperzilla**, an expert biomedical analyst. Your goal is to process ...Votes: 0GitHub stars: 32
- Dashboard每次科研任务开始时，生成一个临时的本地 dashboard，动态展示任务关键信息和产物预览。Votes: 0GitHub stars: 32
- Feishu Rich Card--> --- name: bio-feishu-rich-card description: Send rich interactive cards with embedded images in Feishu group chats. Use when reporting progress, sharing analysis results, or presenting any content that benefits from mixed text+image layout in Feishu. Combines SVG UI templates (or matplotlib/PIL charts) with Feishu Card Kit API. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - ru...Votes: 0GitHub stars: 32
- Svg Ui Templates--> --- name: bio-svg-ui-templates description: Generate professional SVG UI panels for structured information display. Use when presenting lists, task checklists, pipeline/dependency status diagrams, or rich-text report layouts as SVG images. Covers four templates - list-panel, checklist-panel, pipeline-status, richtext-layout. Style is professional, business-oriented, academic-grade with Material Design color palette. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill ...Votes: 0GitHub stars: 32
- Lab Automation--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->Votes: 0GitHub stars: 32
- Codebase Investigator--> --- name: codebase-investigator description: Expertly analyze large codebases to identify patterns, dependencies, and architectural flaws. keywords: - refactoring - analysis - architecture - discovery - search measurable_outcome: Map key components and data flows of a 50k+ LOC repo within 5 minutes, identifying 3+ potential improvements. license: MIT metadata: author: AI Agentic Skills Team version: "2.0.0" compatibility: - system: linux, macos allowed-tools: - list_directory - read_file ...Votes: 0GitHub stars: 32
- GitHub Agentic Workflow--> --- name: github-agentic-workflows description: Configure GitHub's Agentic Workflows technical preview so Copilot, Claude Code, or Codex can act as CI/CD participants with human-in-the-loop safety. keywords: - github-actions - agentic-automation - cicd - repo-maintenance - continuous-ai measurable_outcome: Ship an issue-triage and CI-investigation Agentic Workflow that runs successfully on a target repository within one working session. license: MIT metadata: author: Bioinformatics Oxford...Votes: 0GitHub stars: 32
- Multi Cloud Pricing--> --- name: multi-cloud-pricing description: Compares pricing across major cloud providers (AWS, Azure, GCP, OCI) for various instance types, aiding in cost optimization. keywords: - cloud - pricing - finops - mcp measurable_outcome: Generates a cost comparison report across 3 providers within 2 minutes. license: MIT metadata: author: Software Engineering Tools version: "1.0.0" compatibility: - system: Multi-platform allowed-tools: - run_shell_command --- This skill provides comparative pri...Votes: 0GitHub stars: 32
- R ProgrammingR is a premier language for statistical computing and graphics, serving as the backbone for much of modern bioinformatics, particularly through the Bioconductor project. Mastery of R is essential for genomic data analysis, rigorous statistical testing, and publication-quality visualization.Votes: 0GitHub stars: 32
- Semantic Code Indexing--> --- name: semantic-code-indexing description: Indexes code into a knowledge graph, enabling natural language search, impact analysis, and architectural understanding for AI agents. keywords: - code - indexing - graph - semantic - mcp measurable_outcome: Successfully indexes a target repository and answers structural queries with 95% accuracy. license: MIT metadata: author: Software Engineering Tools version: "1.0.0" compatibility: - system: Multi-platform allowed-tools: - run_shell_comman...Votes: 0GitHub stars: 32
- React Best Practices--> --- name: 'react-best-practices' description: 'A comprehensive guide and rule set for writing clean, performant, and maintainable React code.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command - write_file --- This skill provides a set of architectural and coding standards for React applications. It is designed to be used by agents when generating, refactoring, or reviewing React code to ensure align...Votes: 0GitHub stars: 32
- Spatial Annotate--> --- name: bio-spatial-annotate description: Cell type annotation for spatial transcriptomics data using marker-based scoring, Tangram mapping, scANVI transfer, or CellAssign probabilistic models. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Annotate**, a specialised OmicsClaw agent for cell type annotation. Your role is to assign biolo...Votes: 0GitHub stars: 32
- Spatial Cnv--> --- name: bio-spatial-cnv description: Copy number variation inference from spatial transcriptomics expression data. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial CNV**, a specialised OmicsClaw agent for inferring copy number variations from spatial transcriptomics data. Your role is to detect large-scale chromosomal gains and losses by...Votes: 0GitHub stars: 32
- Spatial Communication--> --- name: bio-spatial-communication description: Cell-cell communication analysis via ligand-receptor interaction scoring using LIANA, CellPhoneDB, FastCCC, or CellChat. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Communication**, a specialised SpatialClaw agent for cell-cell communication analysis in spatial transcriptomics data. You...Votes: 0GitHub stars: 32
- Spatial Condition--> --- name: bio-spatial-condition description: Experimental condition comparison using pseudobulk differential expression with proper multi-sample statistics. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Condition**, a specialised OmicsClaw agent for comparing experimental conditions in spatial transcriptomics data. Your role is to perfo...Votes: 0GitHub stars: 32
- Spatial De--> --- name: bio-spatial-de description: "Differential expression analysis \u2014 find marker genes for clusters\ \ or compare two groups. Supports Wilcoxon rank-sum, t-test, and PyDESeq2 methods\ \ with publication-ready figures and CSV tables." tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial DE**, the differential expression and marker gen...Votes: 0GitHub stars: 32
- Spatial Deconv--> --- name: bio-spatial-deconv description: "Cell type deconvolution for spatial transcriptomics \u2014 estimates\ \ per-spot cell type proportions using FlashDeconv, Cell2Location, RCTD, DestVI,\ \ Stereoscope, Tangram, SPOTlight, or CARD." tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Deconv**, a specialised OmicsClaw agent for cell typ...Votes: 0GitHub stars: 32
- Spatial Domains--> --- name: bio-spatial-domains description: Identify tissue regions and spatial niches from preprocessed spatial transcriptomics data using Leiden, Louvain, SpaGCN, STAGATE, GraphST, or BANKSY. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Domains**, a specialised OmicsClaw agent for tissue region and spatial niche identification. Your r...Votes: 0GitHub stars: 32
- Spatial Enrichment--> --- name: bio-spatial-enrichment description: Pathway and gene set enrichment analysis for spatial transcriptomics data. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Enrichment**, a specialised OmicsClaw agent for pathway and gene set enrichment analysis. Your role is to identify over-represented biological pathways in spatially resolv...Votes: 0GitHub stars: 32
- Spatial Genes--> --- name: bio-spatial-genes description: Find genes with spatially variable expression patterns using Moran's I, SpatialDE, SPARK-X, or FlashS. Identifies genes whose expression is non-randomly distributed across tissue coordinates. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Genes**, the spatially variable gene (SVG) discovery skill ...Votes: 0GitHub stars: 32
- Spatial Integrate--> --- name: bio-spatial-integrate description: Multi-sample integration and batch correction for spatial transcriptomics data. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Integrate**, a specialised OmicsClaw agent for multi-sample integration and batch effect correction. Your role is to align multiple spatial transcriptomics samples int...Votes: 0GitHub stars: 32
- Spatial Preprocess--> --- name: bio-spatial-preprocess description: Load spatial transcriptomics data (Visium, Xenium, MERFISH, Slide-seq, generic h5ad), perform QC filtering, normalization, HVG selection, PCA, UMAP, and Leiden clustering. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Preprocess**, the foundation skill of OmicsClaw spatial analysis. Your rol...Votes: 0GitHub stars: 32
- Spatial Register--> --- name: bio-spatial-register description: Spatial registration and multi-slice alignment for spatial transcriptomics data. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Register**, a specialised OmicsClaw agent for spatial registration and multi-slice alignment. Your role is to align spatial coordinates across serial tissue sections o...Votes: 0GitHub stars: 32
- Spatial Statistics--> --- name: bio-spatial-statistics description: "Comprehensive spatial statistics toolkit \u2014 cluster-level (neighborhood\ \ enrichment, Ripley, co-occurrence), gene-level (Moran's I, Geary's C, local Moran,\ \ Getis-Ord), and network-level analysis." tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Statistics**, the spatial autocorrelati...Votes: 0GitHub stars: 32
- Spatial Trajectory--> --- name: bio-spatial-trajectory description: Trajectory inference and pseudotime analysis for spatial transcriptomics data. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Trajectory**, a specialised OmicsClaw agent for trajectory inference and pseudotime computation in spatial transcriptomics data. Your role is to order cells along deve...Votes: 0GitHub stars: 32
- Spatial Velocity--> --- name: bio-spatial-velocity description: RNA velocity and cellular dynamics analysis for spatial transcriptomics data. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Velocity**, a specialised OmicsClaw agent for RNA velocity analysis in spatial transcriptomics data. Your role is to infer cellular dynamics and directional movement from...Votes: 0GitHub stars: 32
- Bioemu Protein EnsemblesOperate Microsoft BioEmu to sample approximate equilibrium conformational ensembles for protein monomers from amino-acid sequences or supplied MSAs. Use when studying protein flexibility, alternative conformations, free-energy landscapes, disorder, ensemble generation, physical steering, or downstream side-chain reconstruction and MD relaxation.Votes: 0GitHub stars: 32
- Protenix Structure PredictionOperate ByteDance Protenix-v2 for open biomolecular structure prediction of proteins, antibodies, nucleic acids, ligands, and complexes using JSON inputs, MSA and template features, constraints, and inference-time sampling. Use when running Protenix locally or through its server, comparing AlphaFold3-style open models, or building reproducible co-folding evaluations.Votes: 0GitHub stars: 32
- Bulkrna Alignment--> --- name: bio-bulkrna-alignment description: "Bulk RNA-seq count matrix QC \u2014 library size, gene detection rates,\ \ and sample correlation." tool_type: mixed primary_tool: bulkrna measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Library size distribution, gene detection rates, and sample correlation analysis for bulk RNA-seq count matrices.Votes: 0GitHub stars: 32
- Bulkrna Coexpression--> --- name: bio-bulkrna-coexpression description: "WGCNA-style weighted gene co-expression network analysis \u2014 module\ \ detection, soft thresholding, hub genes." tool_type: mixed primary_tool: bulkrna measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- WGCNA-style weighted gene co-expression network analysis. Detects gene modules via soft thresholding, topological overlap, and hierarchical clust...Votes: 0GitHub stars: 32
- Bulkrna De--> --- name: bio-bulkrna-de description: Bulk RNA-seq differential expression analysis using PyDESeq2 with optional edgeR/limma-voom via rpy2. tool_type: mixed primary_tool: bulkrna measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Differential expression analysis for bulk RNA-seq count data. Primary engine is PyDESeq2 (a pure-Python re-implementation of DESeq2); falls back to a scipy Welch's t-test...Votes: 0GitHub stars: 32
- Bulkrna Deconvolution--> --- name: bio-bulkrna-deconvolution description: Bulk RNA-seq cell type deconvolution using NNLS (built-in), with optional CIBERSORTx and MuSiC bridges. tool_type: mixed primary_tool: bulkrna measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Estimate cell type proportions from bulk RNA-seq expression data using non-negative least squares (NNLS). Given a bulk count matrix and a cell type signature...Votes: 0GitHub stars: 32
- Bulkrna Enrichment--> --- name: bio-bulkrna-enrichment description: "Pathway enrichment analysis for bulk RNA-seq \u2014 ORA and GSEA via\ \ GSEApy, with built-in hypergeometric fallback." tool_type: mixed primary_tool: bulkrna measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Pathway enrichment analysis for bulk RNA-seq differential expression results. Primary engine is GSEApy for ORA (Enrichr) and GSEA (pre-ranked);...Votes: 0GitHub stars: 32
- Bulkrna Splicing--> --- name: bio-bulkrna-splicing description: "Alternative splicing analysis \u2014 PSI quantification, differential\ \ splicing event detection from rMATS/SUPPA2 output." tool_type: mixed primary_tool: bulkrna measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Alternative splicing quantification and differential splicing event detection. Accepts pre-computed splicing event tables (e.g. from rMATS o...Votes: 0GitHub stars: 32
- Batch Correction--> --- name: bio-differential-expression-batch-correction description: Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data. tool_type: r primary_tool: sva measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32