plugins

Submit compact NCBI Entrez E-Utilities requests for PubMed, Gene, Protein, Nucleotide, PMC metadata, and GEO metadata workflows. Use when a user wants concise Entrez search, fetch, summary, or link results; save raw JSON or XML only on request.

Submit compact NCBI PMC Open Access requests for article/file availability metadata. Use when a user wants concise PMC Open Access summaries; save raw XML only on request.

Expert guidance for @vercel/ncc — a simple CLI for compiling Node.js modules into a single file with all dependencies included. Use when bundling serverless functions, CLI tools, or any Node.js project into a self-contained file.

Installs NemoClaw, launches a sandbox, and runs the first agent prompt. Use when onboarding, installing, or launching a NemoClaw sandbox for the first time. Trigger keywords - nemoclaw quickstart, install nemoclaw openclaw sandbox, nemohermes quickstart, hermes agent nemoclaw, run hermes openshell sandbox, nemoclaw prerequisites, nemoclaw supported platforms, nemoclaw hardware software, nemoclaw windows wsl2 setup, nemoclaw install windows docker desktop.

next-forge expert guidance — production-grade Turborepo monorepo SaaS starter by Vercel. Use when working in a next-forge project, scaffolding with `npx next-forge init`, or editing @repo/* workspace packages.

Next.js App Router expert guidance. Use when building, debugging, or architecting Next.js applications — routing, Server Components, Server Actions, Cache Components, layouts, middleware/proxy, data fetching, rendering strategies, and deployment on Vercel.

Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt.

Route BCL, FASTQ, BAM/CRAM, count-matrix, or VCF sequencing requests to the right public NGS analysis skill and ask only the missing assay-specific setup questions.

Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows.

Validate Illumina BCL run folders and sample sheets, plan demultiplexing, review index/UMI/lane choices, run BCL-to-FASTQ conversion, and interpret demux metrics while surfacing license/download boundaries.

Dispatch bulk RNA-seq requests to FASTQ-to-count QC or count-matrix differential-expression skills using nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC, and R/Bioconductor workflows.

Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.

Run or plan bulk RNA-seq differential-expression analysis from count matrices with replicate, design formula, contrast, batch, normalization, QC plot, and result-table checks.

Run or plan ChIP-seq, CUT&RUN, or CUT&Tag QC, control handling, spike-in, peak calling, broad-vs-narrow target selection, replicate, bigWig, and differential binding workflows.

Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks.

Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks.

Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.

Dispatch WGS, WES, or targeted DNA variant requests to germline, somatic, or UMI-panel skills, then plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows.

Dispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows.

Validate FASTQ inputs, run local FastQC/MultiQC QC, interpret QC signals, and optionally execute fastp or Cutadapt trimming branches without overwriting raw reads.