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MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis. Use when identifying essential genes, drug targets, or resistance mechanisms from dropout or enrichment screens.

Validates Conductor project artifacts for completeness,

Display project status, active tracks, and next actions

Manage track lifecycle: archive, restore, delete, rename, and cleanup

Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.

Manages connections to Logseq graphs via HTTP API, CLI, or MCP Server. Auto-invokes when users mention connecting to Logseq, API tokens, graph paths, connection issues, or backend configuration. Handles backend detection, environment setup, and connectivity troubleshooting.

Initialize project with Conductor artifacts (product definition,

全球最大的 Claude Code 技能聚合库 · 收录 3900+ 来自 12+ 来源的技能，提供在线搜索与趋势分析看板 / The world's largest Claude Code skill aggregation hub — 3900+ skills from 12+ sources with online search and trend dashboard

Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.

Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via

Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.

Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states.