Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows.
Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile),…
Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features.
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profi — from…
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from met — from…
CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering.
Normalize indel representation, decompose MNPs, and split multiallelic variants using bcftools norm. Use when comparing variants from different callers, preparing VCF for database…
Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautome — from…
Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence score — from…
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a — from…
Root cause analysis for debugging. Use when bugs, test failures, or unexpected behavior have non-obvious causes, or after multiple fix attempts have failed.
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminforma — from…
Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or developmental trajectori — from…
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analys — from…
Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods.
Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired +…
Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and…
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints.
When the user wants to optimize for entity recognition, Knowledge Graph, or entity-based SEO. Also use when the user mentions "entity SEO," "entity optimization," "Knowle — from…
\"Chat UI building blocks for React/Next.js from ui.inference.sh. Components: container, messages, input, typing indicators, avatars.
Patterns and techniques for analyzing brownfield codebases. Use when onboarding to unfamiliar code, preparing for refactoring, conducting architecture reviews, or identifying…
Best practices for writing, reviewing, and refactoring React Flow / @xyflow/react v12 canvases. Use when work touches React Flow components, custom nodes, custom edges, handles,…
Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis.
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignme — from…
Use when executing implementation plans with independent tasks in the current session. Dispatches fresh subagent for each task with code review between tasks.
Calls HLA class I and class II alleles at 2/4/6/8-field resolution from WGS/WES/RNA-seq/long-read data using OptiType, HLA-LA, T1K, Polysolver, HLA-HD, arcasHLA, StarPhase, or…
Jest testing patterns, factory functions, mocking strategies, and TDD workflow. Use when writing unit tests, creating test factories, or following TDD red-green-refactor — from…
End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelian randomization with CHP-aware sensitivity (CAUSE / L — from…
JavaScript/TypeScript ES2024+, async/await, DOM manipulation, Node.js, and API integration. Use when writing vanilla JS/TS code, working with REST/fetch APIs, implementing…
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation diffe — from…
Build production-ready Node.js backend services with Express/Fastify, implementing middleware patterns, error handling, authentication, database integration, and API desi — from…
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations.
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy.
Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes — from…
Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RER — from…
Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.
Fix Chinese/Unicode character encoding issues when running AI agents on Windows via POSIX shells (Git Bash, MSYS2, WSL, BusyBox, etc.).
Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for…
Master Rust async programming with Tokio, async traits, error handling, and concurrent patterns. Use when building async Rust applications, implementing concurrent system — from…
When the user wants to create, optimize, or audit a feedback or roadmap page. Also use when the user mentions "feedback page," "roadmap," "feature requests," "vote on features,"…
Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools…
Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui).
When the user wants to add, optimize, or audit table of contents (TOC) for long-form content. Also use when the user mentions "TOC," "table of contents," "table of contents for…
Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions.
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points).
Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R…
Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes. Four-phase framework ensuring understanding before attempting solutions.
When the user wants to create, optimize, or audit features page content. Also use when the user mentions "features page," "product features," "capabilities," "what it does,"…
When the user wants to plan website structure, decide which pages to build, or prioritize pages for a new or existing site.
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomi — from…
Guides Claude in creating well-structured SKILL.md files following best practices. Provides clear guidelines for naming, structure, and content organization to make skill — from…
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis.
End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expressed cell populations.
Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot…
Search Open Targets drug-disease associations with natural language queries. Target validation powered by Valyu semantic search.
Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.
Generate AI images with FLUX, Gemini, Grok, Seedream, Reve and 50+ models via inference.sh CLI. Models: FLUX Dev LoRA, FLUX.2 Klein LoRA, Gemini 3 Pro Image, Grok Imagine — from…
Software architecture and UI/UX principles for building genuinely new solutions, not derivative work.
Master authentication and authorization patterns including JWT, OAuth2, session management, and RBAC to build secure, scalable access control systems.
Use when creating new skills, editing existing skills, or verifying skills work before deployment — from bg-szy/TOP-SKILLS