Use when starting feature work that needs isolation from current workspace or before executing implementation plans - creates isolated git worktrees with smart directory selection and safety verification
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For...
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic...
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway...
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to...
Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets,...
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...
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Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis,...
Expert guidance for Windows, PowerShell, WSL interop, and cross-platform development
Enhance uxscii components from sketch to production fidelity. Use when working with .uxm files marked as "fidelity: sketch" or when user wants to add detail and polish to components.
Generate web assets including favicons, app icons (PWA), and social media meta images (Open Graph) for Facebook, Twitter, WhatsApp, and LinkedIn. Use when users need icons, favicons, social...
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Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Browse and view all available uxscii components including bundled templates, user components, and screens. Use when working with .uxm files, when user wants to see, list, browse, or search .uxm...
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML,...
Analyze datasets to discover patterns, anomalies, and relationships. Use when exploring data files, generating statistical summaries, checking data quality, or creating visualizations. Supports...
Import UI screenshots and generate uxscii components automatically using vision analysis. Use when user wants to import, convert, or generate .uxm components from screenshots or images.