Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for…
When the user wants to run app install ads, user acquisition (UA), or promote mobile apps. Also use when the user mentions "app ads," "app install ads," "UA," "user acquisition,"…
Linear issue tracking integration - Create, update, and manage Linear issues and projects using the GraphQL API
Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate…
Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent…
End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission infer — from…
Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime…
Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2 to generate gene-level counts for DESeq2/edgeR.
Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturbations in single cells.
Upgrade React applications to latest versions, migrate from class components to hooks, and adopt concurrent features.
Analyze Reddit threads for sentiment, consensus opinions, top arguments, and discussion patterns. Use this when users want to understand Reddit community opinions, analyz — from…
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identif — from…
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints.
When the user wants to create, optimize, or audit alternatives or comparison content (page or blog article).
Execute database migrations across ORMs and platforms with zero-downtime strategies, data transformation, and rollback procedures.
When the user wants to create, optimize, or audit customer stories or case study pages. Also use when the user mentions "case studies," "customer stories," "success stories,"…
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCa — from…
Parallel BMAD workflow orchestration using git worktrees and tmux. USE WHEN BMAD parallel, orchestrate sprint, run stories in parallel, worktree orchestration, sprint…
Guide for implementing Grafana Mimir - a horizontally scalable, highly available, multi-tenant TSDB for long-term storage of Prometheus metrics.
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and — from…
Create commit messages following Sentry conventions. Use when committing code changes, writing commit messages, or formatting git history.
Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without b — from…
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports.
Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST),…
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling.
Manage Supabase projects, databases, migrations, Edge Functions, and storage using the `supabase` CLI.
Comprehensive multi-omics disease characterization integrating genomics, transcriptomics, proteomics, pathway, and therapeutic layers for systems-level understanding.
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, o — from…
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery…
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis.
Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in…
Predict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition.
Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets.
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Word (.docx) manipulation via MCP server. Use for reading, creating, editing, formatting Word documents including tables, footnotes, comments, images, headers, styles, and PDF…
Manage major dependency version upgrades with compatibility analysis, staged rollout, and comprehensive testing.
Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods.
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling.
Comprehensive GitOps methodology and principles skill for cloud-native operations. Use when (1) Designing GitOps architecture for Kubernetes deployments, (2) Implementing — from…
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…
Master error handling patterns across languages including exceptions, Result types, error propagation, and graceful degradation to build resilient applications.
When the user wants to create, optimize, or audit a product listing or category page. Also use when the user mentions "product page," "product listing," "shop," "e-commerce…
Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and — from…
Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC.
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from met — from…
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data.
Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating R — from…
Use when design is complete and you need detailed implementation tasks for engineers with zero codebase context - creates comprehensive implementation plans with exact fi — from…
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize diffe — from…
Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal…
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools.
Notion workspace management via MCP - create databases, pages, comments, and knowledge bases. Use when building Notion documentation, organizing project wikis, or managing Notion…
Deploy applications and websites to Vercel instantly. Use when asked to \"Deploy my app\", \"Deploy this to production\", \"Create a preview deployment\", or \"Push this live\".
Discover genes associated with diseases and traits using GWAS data from the GWAS Catalog (500,000+ associations) and Open Targets Genetics (L2G predictions).
Implement state management patterns for frontend applications. Use when managing global state, handling complex data flows, or coordinating state across components.
Use when doing ANY task involving Supabase. Triggers: Supabase products (Database, Auth, Edge Functions, Realtime, Storage, Vectors, Cron, Queues); client libraries and S — from…
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython.
Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL.