Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter.
Explains machine learning predictions on omics data using SHAP values and LIME for feature attribution. Identifies which genes or features drive classifier decisions.
Implement Linkerd service mesh patterns for lightweight, security-focused service mesh deployments. Use when setting up Linkerd, configuring traffic policies, or implemen — from…
Cloud-based AI swarm deployment and event-driven workflow automation with Flow Nexus platform — from bg-szy/TOP-SKILLS
Design LLM applications using the LangChain framework with agents, memory, and tool integration patterns.
When the user wants to track AI search traffic in GA4 or GSC. Also use when the user mentions "AI traffic," "ChatGPT referral," "Perplexity traffic," "AI Overviews," "GA4 AI…
Research workflow patterns specific to {project}. Covers research agent coordination, source management, and synthesis strategies. — from bg-szy/TOP-SKILLS
Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML.
Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid,…
Transform rough ideas into detailed designs through structured dialogue. Use before implementation to refine requirements.
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation.
Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear…
When the user wants to optimize videos for Google Search, video sitemap, VideoObject schema, or video SEO on websites.
Nominates and assesses CRISPR off-target sites genome-wide. Enumerates candidate sites by mismatch and bulge tolerance with Cas-OFFinder/CRISPRitz, ranks them with the published…
Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib.
Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs.
Ultra-compressed communication mode. Cuts token usage ~75% by dropping filler, articles, and pleasantries while keeping full technical accuracy.
When the user wants to create, audit, or optimize sitemap.xml. Also use when the user mentions "sitemap," "sitemap.xml," "sitemap index," "lastmod," "changefreq," "priority," "URL…
Comprehensive toolkit for product managers including RICE prioritization, customer interview analysis, PRD templates, discovery frameworks, and go-to-market strategies.
Profile and optimize Python code using cProfile, memory profilers, and performance best practices. Use when debugging slow Python code, optimizing bottlenecks, or improvi — from…
Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt.
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM file — from…
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking.
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets — from…
Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq,…
Create AI avatar, talking-head, and lip-sync videos on RunComfy via the `runcomfy` CLI. Routes across ByteDance OmniHuman (audio-driven full-body avatar), Wan-AI Wan 2-7…
When the user wants to run native ads on Taboola, Outbrain, or similar platforms. Also use when the user mentions "native ads," "Taboola," "Outbrain," "content recommendation,"…
Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic…
When the user faces brand impersonation, fake websites, phishing sites, or trademark infringement. Also use when the user mentions "fake site," "impersonation," "phishing site,"…
Generate descriptive commit messages by analyzing git diffs. Use when the user asks for help writing commit messages or reviewing staged changes. — from bg-szy/TOP-SKILLS
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignmen — from…
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex re — from…
Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types.
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
When the user wants to validate product-market fit, measure PMF, or plan before scaling. Also use when the user mentions "PMF," "product-market fit," "product market fit," "Sean…
Create AI avatar and talking head videos via inference.sh CLI. Recommended: P-Video-Avatar (fastest, cheapest, built-in TTS). Also: OmniHuman, Fabric, PixVerse.
Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen…
Generate AI videos with Google Veo, Seedance, Wan, Grok and 40+ models via inference.sh CLI. Models: Veo 3.1, Veo 3, Seedance 1.5 Pro, Wan 2.5, Grok Imagine Video, OmniHu — from…
Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, mixed), Hochberg/Hommel/Holm with…
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools.
Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program…
Use when completing tasks, implementing major features, or before merging to verify work meets requirements — from bg-szy/TOP-SKILLS
World-class data engineering skill for building scalable data pipelines, ETL/ELT systems, and data infrastructure.
Execute Python code in a safe sandboxed environment via [inference.sh](https://inference.sh). Pre-installed: NumPy, Pandas, Matplotlib, requests, BeautifulSoup, Selenium — from…
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation.
Enforces local testing before any deployment. MUST be used before running vercel, git push, or any deployment command. Prevents deploying untested code.
Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods.
Create and manage Claude Code skills following Anthropic best practices. Use when creating new skills, modifying skill-rules.json, understanding trigger patterns, working — from…
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative trait — from…
Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering,…
Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish,…
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided — from…
Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation.
Optimize Apache Spark jobs with partitioning, caching, shuffle optimization, and memory tuning. Use when improving Spark performance, debugging slow jobs, or scaling data — from…
Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1.
Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens…
Systematically debug code issues using proven methodologies. Use when encountering errors, unexpected behavior, or performance problems.
Generate comprehensive disease research reports using 100+ ToolUniverse tools. Creates a detailed markdown report file and progressively updates it with findings from 10 research…
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel.