jackspace
Publisher on askill
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRN...
Analyze datasets to discover patterns, anomalies, and relationships. Use when exploring data files, generating statistical summaries, checking data quality, or creating visualizations. Supports CSV, E...
Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel workflows.
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 analysis. F...
Use when tests have race conditions, timing dependencies, or inconsistent pass/fail behavior - replaces arbitrary timeouts with condition polling to wait for actual state changes, eliminating flaky te...
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.
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, mzIdentML),...
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
Expert guidance for Git workflows, troubleshooting, and best practices
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Complete knowledge domain for Cloudflare D1 - serverless SQLite database on Cloudflare's edge network. Use when: creating D1 databases, writing SQL migrations, configuring D1 bindings, querying D1 fr...
Backend AI functionality with Vercel AI SDK v5 - text generation, structured output with Zod, tool calling, and agents. Multi-provider support for OpenAI, Anthropic, Google, and Cloudflare Workers AI....
Work with MongoDB (document database, BSON documents, aggregation pipelines, Atlas cloud) and PostgreSQL (relational database, SQL queries, psql CLI, pgAdmin). Use when designing database schemas, wri...
Expert guidance for Stable Diffusion image generation, optimization, and troubleshooting.
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
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