Advanced ArgoCD operations beyond the core CLI/API — multi-cluster ApplicationSet generators, automated image updates, new-cluster bootstrapping, and workload onboarding via…
When the user wants to add or optimize trust badges, "Trusted by" logos, security seals, or social proof elements.
When the user wants to run display, banner, or ad network campaigns. Also use when the user mentions "display ads," "banner ads," "ad network," "ad alliance," "programmatic…
Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero.
Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds.
Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods.
Extract medical entities (symptoms, medications, lab values, diagnoses) from patient messages.
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information.
End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate…
Generates detailed chapter outlines for books, including key scenes, plot progression, character arcs, and themes. Use this when planning book structure or expanding story ideas.
End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regulatory-compliant reporting.
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV.
Expert patterns for Neon serverless Postgres, branching, connection pooling, and Prisma/Drizzle integration Use when: neon database, serverless postgres, database branchi — from…
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…
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
Design and implement event stores for event-sourced systems. Use when building event sourcing infrastructure, choosing event store technologies, or implementing event per — from…
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome. — from bg-szy/TOP-SKILLS
Master advanced Git workflows including rebasing, cherry-picking, bisect, worktrees, and reflog to maintain clean history and recover from any situation.
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification.
Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath- — from…
Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Genomics scATAC data, perform QC, dimensionality reduction, clustering, peak calling, and moti — from…
Use when starting feature work that needs isolation from current workspace or before executing implementation plans - creates isolated git worktrees with smart directory — from…
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening an — from…
Implement modern responsive layouts using container queries, fluid typography, CSS Grid, and mobile-first breakpoint strategies.
Compare GWAS studies, perform meta-analyses, and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog and Open Targets Genetics to compare study designs, effect…
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library fi — from…
Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as…
Senhasegura PAM platform integration — A2A OAuth 2.0, PAM Core credentials, SSH key rotation, DSM CLI for CI/CD, External Secrets Operator (Kubernetes), MySafe, and a runnable MCP…
Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment.
Run 250+ AI apps via inference.sh CLI - image generation, video creation, LLMs, search, 3D, Twitter automation.
Implement NFT standards (ERC-721, ERC-1155) with proper metadata handling, minting strategies, and marketplace integration.
Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel.
Master systematic debugging techniques, profiling tools, and root cause analysis to efficiently track down bugs across any codebase or technology stack.
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, gener — from…
When the user wants to plan, create, or market a podcast. Also use when the user mentions "podcast," "podcast strategy," "podcast SEO," "show notes," "podcast distributio — from…
Azure FinOps reservation analysis, cost validation, waste discovery, and executive reporting. USE WHEN user says 'validate costs', 'check reservations', 'find waste', 'orphaned…
Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance),…
Create isolated git worktrees with smart directory selection and safety verification. Use this when starting feature work that needs isolation, parallel development, or s — from…
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal — from…
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that — from…
Master advanced AgentDB features including QUIC synchronization, multi-database management, custom distance metrics, hybrid search, and distributed systems integration.
Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1…
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal — from…
Perform comprehensive audit of interface quality across accessibility, performance, theming, and responsive design.
Complete Git workflow from conventional commits to pre-completion verification. Use for all Git operations including commits, branches, and releases.
Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant.
Debug regex patterns with visual breakdowns, plain English explanations, test case generation, and flavor conversion.
End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV — from…
Use when building App Store screenshot pages, generating exportable marketing screenshots for iOS apps, or creating programmatic screenshot generators with Next.js.
Implement JSON-based structured logging for observability. Use when setting up logging, debugging production issues, or preparing for log aggregation (ELK, Datadog).
Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific…
Automate Twitter/X with posting, engagement, and user management via inference.sh CLI. Apps: x/post-tweet, x/post-create (with media), x/post-like, x/post-retweet, x/dm-s — from…
Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
When the user wants to design, optimize, or audit hero sections (above-the-fold main visual area). Also use when the user mentions "hero," "hero section," "hero area," "above the…
Run the Gemini file processor on any folder — extracts content from PDF, PPTX, XLSX, DOCX, CSV, JSON, and any text format, then generates Obsidian-ready summaries.
Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue),…
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck.
Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and…
Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery.