Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter.
Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for animation, with awareness of current Kaleido static-export model…
Invoke external AI CLIs via native Task agents (Claude, Codex, Gemini, Cursor). Primary mode for multi-provider orchestration with fork-terminal fallback for auth.
Gene and region-based rare-variant aggregation - burden/collapsing, SKAT, SKAT-O, ACAT-V/ACAT-O, annotation-weighted STAAR - with regenie (--vc-tests), SAIGE-GENE+, and t — from…
Use the LI.FI REST API for cross-chain and same-chain token swaps, bridging, DeFi deposits through Composer, yield discovery and position tracking through Earn, and solver-based…
Help developers write code that interacts with Alkahest escrow contracts using the TypeScript, Rust, or Python SDK — from bg-szy/TOP-SKILLS
Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures — from…
Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease con — from…
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks.
Implement saga patterns for distributed transactions and cross-aggregate workflows. Use when coordinating multi-step business processes, handling compensating transactions, or…
Install strict Xcode Makefile tooling for iOS/macOS projects, including build/run/test scripts with AGENT_NAME-based per-agent isolation under build/.
Render videos from React/Remotion component code via inference.sh. Pass TSX code, get MP4. Supports all Remotion APIs: useCurrentFrame, useVideoConfig, spring, interpolat — from…
\"Declarative UI widgets from JSON for React/Next.js from ui.inference.sh. Render rich interactive UIs from structured agent responses.
Verify whether an image or video is authentic, original and correctly captioned — provenance checks, error level analysis, noise and JPEG compression analysis, clone and copy-move…
When the user wants to design, optimize, or audit carousel/slider layouts for content display. Also use when the user mentions "carousel," "slider," "carousel layout,"…
Convert an existing frontend into Stitch-ready design assets by extracting static HTML, writing DESIGN.md, creating the design system, and uploading approved files.
Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods.
Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing sk — from…
Extend or continue an existing video clip on RunComfy via the `runcomfy` CLI. Routes to Google Veo 3-1's `extend-video` and `fast/extend-video` endpoints — pick the sourc — from…
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-saf — from…
Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment.
Batteries-included agent component for React/Next.js from ui.inference.sh. One component with runtime, tools, streaming, approvals, and widgets built in.
Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review.
Run 150+ AI apps via inference.sh CLI - image generation, video creation, LLMs, search, 3D, Twitter automation.
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels).
Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction.
Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor…
Guide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical specs, decision docs, or simila — from…
Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza,…
Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers.
Comprehensive spreadsheet creation, editing, and analysis with support for formulas, formatting, data analysis, and visualization.
Transform data into compelling narratives using visualization, context, and persuasive structure. Use when presenting analytics to stakeholders, creating data reports, or — from…
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython.
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating — from…
Review homework notebooks for completeness, reproducibility, safe execution, and academic-integrity boundaries.
Reconcile a recorded home-bar inventory against supplied physical bottle observations. Use after purchases, use, moves, or a long gap when every record and observation needs one…
Generate cinematic short-form video with ByteDance Seedance 2.0 Pro on RunComfy. Documents Seedance 2.0 Pro's strengths (multi-modal references — up to 9 images, 3 videos — from…
Turns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi (RGChannelSet -> MethylSet ->…
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation.
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized),…
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto. — from bg-szy/TOP-SKILLS
Conduct comprehensive deep research on any topic using Dify-powered workflow - searches documentation, academic papers, tutorials, APIs, best practices, and returns struc — from…
Git operations, shell scripting, CI/CD pipelines, and terminal automation. Use for conventional commits, PowerShell/Bash scripting, configuring GitHub Actions, or automating…
When the user wants to create, optimize, or audit a careers or jobs page. Also use when the user mentions "careers," "jobs," "hiring," "open positions," "company culture,"…
Professional web application testing and automation using Playwright with support for multiple browsers, mobile emulation, screenshot capture, network interception, and…
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis.
Shell script static analysis and linting. USE WHEN shellcheck, lint shell, bash lint, sh lint, script analysis, shell errors, SC codes, shell best practices.
Use when creating new skills, editing existing skills, or verifying skills work before deployment — from bg-szy/TOP-SKILLS
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing.
Draft, prepare, publish, and verify personal or project LinkedIn posts through the user's signed-in Chrome session, including audience review, public-safe media uploads, links,…
Next-generation sequencing data analysis pipelines including bulk RNA-seq, scRNA-seq preprocessing, variant calling, and quality control.
AI image generation for agents: text-to-image and prompt-to-image through Image Skill's zero-setup hosted runtime.
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, al — from…
Modern SwiftUI toolbar patterns including customizable toolbars, search integration, transition effects, and platform-specific behavior.
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy.
Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site…
Migrate MS Teams chat content to channels or between chats. USE WHEN teams migration, migrate chat, copy messages, teams channel, move chat history, teams backup, chat to channel.
Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python).
You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior.