Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
Conduct enterprise-grade research with multi-source synthesis, citation tracking, and verification. Use when user needs comprehensive analysis requiring 10+ sources, veri — from…
Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon — from…
Microsoft docs lookup, code samples, and SDK reference for Azure, .NET, Microsoft 365, Windows, and Power Platform via Microsoft Learn MCP.
Guide for creating MCP (Model Context Protocol) servers. Use this when building integrations with external services, creating new MCP servers, or connecting Claude to APIs.
Extract and analyze data from invoices, receipts, bank statements, and financial documents. Categorize expenses, track recurring charges, and generate expense reports.
When the user wants to optimize signup, registration, account creation, or trial activation flows. Also use when the user mentions "signup conversions," "registration fri — from…
Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, signific — from…
Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles,…
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
WordPress Playground for instant browser-based WordPress testing. Use for quick demos, plugin testing, or ephemeral development environments without Docker.
Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus),…
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and b — from…
Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes — from…
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample s — from…
Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying — from…
Opinionated frontend development standards for modern React + TypeScript applications. Covers Suspense-first data fetching, lazy loading, feature-based architecture, MUI v7…
Master advanced prompt engineering techniques to maximize LLM performance, reliability, and controllability in production.
Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.
Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples.
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts.
Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm,…
Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution…
Execute implementation plans with batch processing and review checkpoints. Use when given a plan document.
Create well-formatted git commits with conventional commit messages and emoji. Use when user asks to commit changes, save work, or after completing a task that should be committed.
Manage Git workflows including commits, branches, merges, and collaboration. Use when working with Git repositories, creating commits, managing branches, or resolving conflicts.
Use when about to claim work is complete, fixed, or passing, before committing or creating PRs - requires running verification commands and confirming output before makin — from…
Generate commit messages following project conventions for staged changes. Use when the user asks to commit changes or run /commit.
Generate AI images with GPT-Image-2, FLUX, Gemini, Grok, Seedream, Reve and 50+ models via inference.sh CLI.
Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces.
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis.
Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de…
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing.
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream ana — from…
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected…
Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles, interprets PRS percentiles, and assesses…
Transform podcast transcripts into comprehensive content marketing suites including blog posts, social media content, newsletters, SEO-optimized articles, and timestamps — from…
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package.
Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon — from…
Comprehensive Docker containerization workflow covering multi-stage builds, docker-compose orchestration, image optimization, debugging, and production best practices.
When the user wants to run YouTube ads, set up TrueView or Bumper campaigns, or optimize video ad creative.
Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content.
Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge…
\"Tool lifecycle UI components for React/Next.js from ui.inference.sh. Display tool calls: pending, progress, approval required, results.
Generates creative domain name ideas for your project and checks availability across multiple TLDs (.com, .io, .dev, .ai, etc.).
WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways.
Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO,…
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequenc — from…
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis.
Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery.
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments. — from bg-szy/TOP-SKILLS
Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data.
Redesign or QA PDFs for clarity while preserving IDs, dates, amounts, barcodes, QR codes, seals, signatures, labels, and meaning.
Analyze datasets to extract insights, identify patterns, and generate reports. Use when exploring data, creating visualizations, or performing statistical analysis.
Define and implement Service Level Indicators (SLIs) and Service Level Objectives (SLOs) with error budgets and alerting.
Frontend development guidelines for Next.js + React 19 + shadcn/ui applications. Modern patterns including App Router, Server Components, Client Components, Server Action — from…
Master defensive Bash programming techniques for production-grade scripts. Use when writing robust shell scripts, CI/CD pipelines, or system utilities requiring fault tol — from…
Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC…
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.