Claude Skills by majiayu000

Finds differentially expressed genes (markers) for clusters of T/B cells using Seurat's FindMarkers function. Performs statistical testing between clusters, identifies cluster-defining genes, and automatically runs pathway enrichment analysis (via Enrichr) on significant markers. Generates publication-ready visualizations including volcano plots, dot plots, heatmaps, and enrichment plots.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

SOTA Computer Vision Expert (2026). Specialized in YOLO26, Segment Anything 3 (SAM 3), Vision Language Models, and real-time spatial analysis.

This skill provides guidance for counting tokens in datasets using specific tokenizers. It should be used when tasks involve tokenizing dataset content, filtering data by domain or category, and aggregating token counts. Common triggers include requests to count tokens in HuggingFace datasets, filter datasets by specific fields, or use particular tokenizers (e.g., Qwen, DeepSeek, GPT).

Process data normalization tool operations. Auto-activating skill for ML Training. Triggers on: data normalization tool, data normalization tool Part of the ML Training skill category. Use when working with data normalization tool functionality. Trigger with phrases like "data normalization tool", "data tool", "data".

Process data normalization tool operations. Auto-activating skill for ML Training. Triggers on: data normalization tool, data normalization tool Part of the ML Training skill category. Use when working with data normalization tool functionality. Trigger with phrases like "data normalization tool", "data tool", "data".

Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Build a rigorous world model with state, dynamics, uncertainty, and provenance. Use when creating digital twins, constructing system representations, building simulation foundations, or establishing baseline world state.

Synchronize construction digital twins with real-time data. Connect BIM models with IoT sensors, progress updates, and field data for live project visualization and monitoring.

Build and maintain digital twins - virtual representations of physical systems that synchronize with real-world counterparts for monitoring, prediction, and optimization. Use when "digital twin, virtual model, real-time synchronization, physical-virtual coupling, predictive maintenance, asset modeling, system replica, live simulation, " mentioned.

Build transformer fine-tuning run plans with task settings, hyperparameters, and model-card outputs. Use for repeatable Hugging Face or PyTorch finetuning workflows.

Select and optimize embedding models for semantic search and RAG applications. Use when choosing embedding models, implementing chunking strategies, or optimizing embedding quality for specific domains.

Select and optimize embedding models for semantic search and RAG applications. Use when choosing embedding models, implementing chunking strategies, or optimizing embedding quality for specific domains.

Select and optimize embedding models for semantic search and RAG applications. Use when choosing embedding models, implementing chunking strategies, or optimizing embedding quality for specific domains.

Evaluation framework patterns for RAG and LLMs, including faithfulness metrics, synthetic dataset generation, and LLM-as-a-judge patterns. Triggers: ragas, deepeval, llm-eval, faithfulness, hallucination-check, synthetic-data.

Evaluation framework patterns for RAG and LLMs, including faithfulness metrics, synthetic dataset generation, and LLM-as-a-judge patterns. Triggers: ragas, deepeval, llm-eval, faithfulness, hallucination-check, synthetic-data.

Measure model performance on test datasets. Use when assessing accuracy, precision, recall, and other metrics.

All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.

All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.

Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.

Auto-generate features with encodings, scaling, polynomial features, and interaction terms for ML pipelines.

Create and transform features using encoding, scaling, polynomial features, and domain-specific transformations for improved model performance and interpretability

Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

Guide for implementing Google Gemini API image understanding - analyze images with captioning, classification, visual QA, object detection, segmentation, and multi-image comparison. Use when analyzing images, answering visual questions, detecting objects, or processing documents with vision.

Guide for implementing Google Gemini API image understanding - analyze images with captioning, classification, visual QA, object detection, segmentation, and multi-image comparison. Use when analyzing images, answering visual questions, detecting objects, or processing documents with vision.

Guide for implementing Google Gemini API image understanding - analyze images with captioning, classification, visual QA, object detection, segmentation, and multi-image comparison. Use when analyzing images, answering visual questions, detecting objects, or processing documents with vision.

Guide for implementing Google Gemini API image understanding - analyze images with captioning, classification, visual QA, object detection, segmentation, and multi-image comparison. Use when analyzing images, answering visual questions, detecting objects, or processing documents with vision.

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

Problem-solving strategies for gradient methods in optimization

Problem-solving strategies for gradient methods in optimization

Python library for building ML demo UIs with minimal code. Create interactive web interfaces for models with text, image, audio, and video inputs/outputs. Share demos via public links or deploy to Hugging Face Spaces.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Execute Hugging Face Hub operations using the `hf` CLI. Use when the user needs to download models/datasets/spaces, upload files to Hub repositories, create repos, manage local cache, or run comput...

This skill should be used when users want to train or fine-tune language models using TRL (Transformer Reinforcement Learning) on Hugging Face Jobs infrastructure. Covers SFT, DPO, GRPO and reward modeling training methods, plus GGUF conversion for local deployment. Includes guidance on the TRL Jobs package, UV scripts with PEP 723 format, dataset preparation and validation, hardware selection, cost estimation, Trackio monitoring, Hub authentication, and model persistence. Should be invoked f...

Use when the user is doing AI/ML work in a scientific domain — biology, chemistry, physics, astronomy, climate, genomics, materials science, medicine, ecology, energy, conservation, engineering, mathematics, scientific reasoning, drug discovery, protein design, weather modeling, theorem proving, single-cell, PDE solving, or anything similar. Hugging Science (huggingscience.co) is a curated catalog of scientific datasets, models, blog posts, and interactive Spaces; the `hugging-science` org on...

Use Hugging Face Transformers for local model inference, embeddings, and fine-tuning. Covers pipelines, model selection, quantization, and optimization. Use when working with local LLMs, embeddings, or custom model training.

Debug Gemini/GPT vision API issues in puzzle image extraction

Debug Gemini/GPT vision API issues in puzzle image extraction

Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training classifiers or validating automated phenotyping results.

K-Scale kinfer model inference engine for deploying trained RL policies to real robots via ONNX Runtime in Rust

Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation.

Five-skill sequence for 'what am I missing?' - Collide → Critique → Scale → Synthesize → Simplify. Use when you suspect you're not seeing something.