Search: "matched"

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.

Analyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific skills, and stage new skill drafts or composition recipes for review. Requires a reachable Screenpipe HTTP API, normally on localhost:3030. Detection and embedding inference run locally; the selected LLM receives redacted app/title cluster summaries and matched skill descriptions. Use only when the user explicitly asks to analyze their recent work and propose skills.

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.

Audits a project's dependencies for supply-chain risk: version-matched advisories for direct dependencies and the full lockfile tree, abandoned or archived upstreams, npm publisher concentration, and install-time script execution. Use when asked to audit dependencies, assess supply-chain or third-party package risk, or review a dependency tree before an engagement.

Expo's official example projects - the expo/examples repo of ~70 `with-*` integrations (Stripe, Clerk, Supabase, OpenAI, maps, Reanimated, SQLite, Skia, NativeWind, and more). Use when integrating a third-party library or service into an existing Expo app and you want the canonical, version-matched pattern to adapt, or when scaffolding a new project from one with `npx create-expo --example`.