Documentation

Docs, README files, API references, tutorials, specs, and changelogs

skills in category: 15,624
pages available: 651

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Showing 10,153–10,176 of 15,624 skills

QutipA--> --- name: bio-qutip description: "Quantum physics simulation library for open quantum systems. Use when\ \ studying master equations, Lindblad dynamics, decoherence, quantum optics, or\ \ cavity QED. Best for physics research, open system dynamics, and educational simulations.\ \ NOT for circuit-based quantum computing\u2014use qiskit, cirq, or pennylane for\ \ quantum algorithms and hardware execution." tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow suc...documentationpythongoVotes: 0GitHub stars: 32
PysamA--> --- name: bio-pysam description: Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing 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 ---documentationpythonshellVotes: 0GitHub stars: 32
PydicomA--> --- name: bio-pydicom description: Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving...documentationpythonrustVotes: 0GitHub stars: 32
Molecular DynamicsA--> --- name: bio-molecular-dynamics description: Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tool...documentationpythonphpVotes: 0GitHub stars: 32
Metabolomics Workbench DatabaseA--> --- name: bio-metabolomics-workbench-database description: 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. 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 ---documentationpythonshellVotes: 0GitHub stars: 32
MatlabA--> --- name: bio-matlab description: MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB ...documentationpythongoVotes: 0GitHub stars: 32
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Markdown Mermaid WritingA--> --- name: bio-markdown-mermaid-writing description: Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. all...documentationpythongoVotes: 0GitHub stars: 32
Gnomad DatabaseA--> --- name: bio-gnomad-database description: Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_c...documentationpythongoVotes: 0GitHub stars: 32
Gene DatabaseA--> --- name: bio-gene-database description: Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis. 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 ---documentationpythongoVotes: 0GitHub stars: 32
EtetoolkitA--> --- name: bio-etetoolkit description: Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics. 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 ---documentationpythonshellVotes: 0GitHub stars: 32
Ensembl DatabaseA--> --- name: bio-ensembl-database description: Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research. 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 ---documentationpythongoVotes: 0GitHub stars: 32
Ena DatabaseA--> --- name: bio-ena-database description: Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats. 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 ---documentationpythonshellVotes: 0GitHub stars: 32
Cosmic DatabaseA--> --- name: bio-cosmic-database description: Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication. 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 ---documentationpythonshellVotes: 0GitHub stars: 32
Clinpgx DatabaseA--> --- name: bio-clinpgx-database description: Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions. 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 ---documentationpythongoVotes: 0GitHub stars: 32
Clinicaltrials DatabaseA--> --- name: bio-clinicaltrials-database description: Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching. 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 ---documentationpythongoVotes: 0GitHub stars: 32
Chembl DatabaseA--> --- name: bio-chembl-database description: Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry. 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 ---documentationpythongoVotes: 0GitHub stars: 32
Markers AnnotationA--> --- name: bio-single-cell-markers-annotation description: Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for differential expression between clusters, identifying cluster-specific markers, scoring gene sets, and assigning cell type labels. Use when finding marker genes and annotating clusters. tool_type: mixed primary_tool: Seurat measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed...documentationpythonshellVotes: 0GitHub stars: 32
Skill CreatorA--> --- name: 'skill-creator' description: 'Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude''s capabilities with specialized knowledge, workflows, or tool integrations.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill provides guidance for creating effective skills.documentationpythongoVotes: 0GitHub stars: 32
Notion Knowledge CaptureA--> --- name: 'notion-knowledge-capture' description: 'Transforms conversations and discussions into structured documentation pages in Notion. Captures insights, decisions, and knowledge from chat context, formats appropriately, and saves to wikis or databases with proper organization and linking for easy discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Transforms conversations, discussi...documentationgoshellVotes: 0GitHub stars: 32
Mcp BuilderA--> --- name: 'mcp-builder' description: 'Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---documentationtypescriptpythonVotes: 0GitHub stars: 32
Consensus InterpretALLM-grounded biological interpretation of a verified typed consensus run. Reads the typed run dir + the original adata, runs inline per-cluster DE, looks up markers in a bundled tissue-keyed marker DB, and asks the chair LLM to (γ) name each cluster's likely cell type with mandatory marker citations and (β) recommend top-3 next-step skills with mandatory evidence_refs. Output banner [A+I: Interpreted on verified consensus]. Failure-mode contract per ADR 0012.documentationbashexpressVotes: 0GitHub stars: 32
Sc In Silico PerturbationALoad when predicting in-silico gene knockout effects on a normalised scRNA AnnData via GRN-based propagation (Python) or scTenifoldKnk (R). Skip when you have a real Perturb-seq / CRISPR screen (use sc-perturb / sc-perturb-prep) or for predicting drug sensitivity (use sc-drug-response).documentationpythongoVotes: 0GitHub stars: 32
Sc Drug ResponseALoad when scoring drug sensitivity per cluster on an annotated scRNA AnnData via simple-correlation against drug-target signatures or via CaDRReS-Sc pretrained models (GDSC / PRISM). Skip when the AnnData has no cluster labels yet (run sc-clustering first) or for predicting genetic-perturbation effects (use sc-in-silico-perturbation).documentationpythongoVotes: 0GitHub stars: 32
Sc Cell AnnotationALoad when assigning cell-type labels to a clustered scRNA AnnData via marker dictionaries, CellTypist, PopV, KNNPredict, SingleR, scmap, SCSA, or a manual cluster-to-label map. Skip when ranking marker genes per cluster (use sc-markers) or for condition-vs-control DE (use sc-de).documentationpythongoVotes: 0GitHub stars: 32