Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC.
Automated code review with security scanning, quality metrics, and best practices analysis. Use when reviewing code for: (1) Security vulnerabilities and common attack vectors,…
Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional…
Master dbt (data build tool) for analytics engineering with model organization, testing, documentation, and incremental strategies.
Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and…
Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis.
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery.
Design multi-stage CI/CD pipelines with approval gates, security checks, and deployment orchestration.
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables.
Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures.
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building anno — from…
Automates browser interactions for web testing, form filling, screenshots, and data extraction. Use when the user needs to navigate websites, interact with web pages, fil — from…
Automates browser interactions for web testing, form filling, screenshots, and data extraction. Use when the user needs to navigate websites, interact with web pages, fil — from…
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.
Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol),…
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation diffe — from…
Create generative art using p5.js with seeded randomness. Use this when creating procedural art, interactive visualizations, or algorithmic designs.
Downloads videos from YouTube and other platforms for offline viewing, editing, or archival. Handles various formats and quality options. — from bg-szy/TOP-SKILLS
When the user wants to decide domain structure for multiple products or brands—subfolder vs subdomain vs independent domain.
Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.
RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics.
Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs.
Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
Comprehensive spreadsheet creation, editing, and analysis with support for formulas, formatting, data analysis, and visualization.
Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features.
Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA + protein or RNA + ATAC — from…
Search medRxiv medical preprints with natural language queries. Powered by Valyu semantic search.
Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein /…
Expert at integrating Model Context Protocol (MCP) servers into Claude Code plugins. Auto-invokes when the user wants to add external tool integrations, configure MCP servers, set…
Implement DeFi protocols with production-ready templates for staking, AMMs, governance, and lending systems.
Plan lifecycle management for Codex plans stored in $CODEX_HOME/plans (default ~/.codex/plans). Use when a user asks to create, find, read, update, delete, or manage plan…
Create and manage production Grafana dashboards for real-time visualization of system and application metrics.
Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering,…
Robusta Kubernetes observability and alert automation platform. USE WHEN installing Robusta OR configuring playbooks OR setting up notification sinks OR troubleshooting Kubernetes…
Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (U — from…
Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4…
Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.
Interactive Obsidian vault configurator. USE WHEN setting up obsidian vault, creating second brain, initializing knowledge base, new vault, vault bootstrap, configure obsidian,…
Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or…
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker.
Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assa — from…
Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research.
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis. — from bg-szy/TOP-SKILLS
When the user wants to create, optimize, or audit FAQ page content. Also use when the user mentions "FAQ page," "frequently asked questions," "help page," "Q&A page," "FAQ…
Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and…
When the user wants to optimize brand search for a company with multiple domains (e.g. parent company.com vs product.ai).
Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling.
Documentation quality standards and writing principles. Use when establishing formatting rules, reviewing doc quality metrics, creating writing guidelines, or enforcing consistent…
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images.
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality sc — from…
World-class prompt engineering skill for LLM optimization, prompt patterns, structured outputs, and AI product development.
Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of…
Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows).
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any se — from…
Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes - four-phase framework (root cause investigation, pattern analysis, hypothesis — from…
Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror.
Build tools that agents can use effectively, including architectural reduction patterns — from bg-szy/TOP-SKILLS
Complete code review workflow for both requesting and receiving reviews. Use when creating PRs, reviewing code, or responding to feedback.
Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (windowed depth, cumulative distribution, --quantize callable…
Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison.