mims-harvard
Publisher on askill
Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic lethal interactions,...
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinica...
Optimize ToolUniverse skills for better report quality, evidence handling, and user experience. Apply patterns like tool verification, foundation data layers, disambiguation-first, evidence grading, q...
Systematic clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Aggregates evidence from ClinVar, gnomAD, CIViC, UniProt, and PDB...
Identify drug repurposing candidates using ToolUniverse for target-based, compound-based, and disease-driven strategies. Searches existing drugs for new therapeutic indications by analyzing targets, b...
Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering. Handles multi-factor...
Orchestrate the full ToolUniverse self-improvement cycle: discover APIs, create tools, test with researcher personas, fix issues, optimize skills, and push via git. References and dispatches to all ot...
Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms. Performs spatial clustering, domain i...
Transform GWAS signals into actionable drug targets and repurposing opportunities. Performs locus-to-gene mapping, target druggability assessment, existing drug identification, safety profile evaluati...
GitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests, and cleaning staged files. Use when pushing to GitHub, fixing CI failures, or clea...
Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology. Integrates tools from ToolUniverse's 1,264+ tool library, creates missing tools when needed, tests t...
Code quality patterns and guidelines for ToolUniverse tool development. Apply when writing, fixing, or refactoring tool Python code in the ToolUniverse project. Encodes lessons from 80+ debug rounds....
Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUniverse tools fail tests, return errors, have schema va...
Detect and auto-install missing ToolUniverse research skills by checking common client skill directories and cloning from GitHub if absent. Use when ToolUniverse specialized skills are not installed,...
Install and configure ToolUniverse with MCP integration for any AI coding client (Cursor, Claude Desktop, Windsurf, VS Code, Codex, Gemini CLI, Trae, Cline, Antigravity, OpenCode, etc.). Covers uv/uvx...
Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities for causal variants, links variants to genes via L2G...
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