Helps construct RwEq (rewrite equivalence) proofs using transitivity, congruence, and canonical lemmas from the LND_EQ-TRS system. Use when proving path equalities, working with quotients, or establishing rewrite equivalences in the ComputationalPaths library.
RFdiffusion3 protein design reference. Use when working with RFD3, contigs, symmetry, hotspots, fixed atoms, RASA conditioning, H-bond conditioning, or Foundry API. Covers all input parameters, design types, and best practices.
Execute the complete dsRNA design workflow with human confirmation at each step
Python-based single cell analysis using Scanpy for .h5ad files in conda scanpy environment
This skill should be used when the user asks to analyze, filter, or inspect VCF/BCF variant files from WGS/WES sequencing. Triggers include requests to calculate variant statistics, filter variants by quality/depth/frequency, extract variants from specific chromosomes or regions, or export variant data as JSON for downstream analysis.
Screen dsRNA candidates for off-target matches in human and honeybee
scArches 单细胞深度学习参考图谱框架 - 100%覆盖文档（26个HTML文件，包含完整API、教程、模型训练、多模态整合）
Liana-py 细胞互作分析工具包 - 100%覆盖文档（60个核心文件+72个图片文件）
GPU-accelerated correlation matrix computation with persistent SQLite caching to eliminate bottleneck at correlation calculation during symbol selection
Organ Axis tutorial docs - 100%覆盖文档（模型应用+公式+注释采样+教程)
Fill gaps between checkpoints using hybrid GPS (70%) + address (30%) template matching with high confidence
Download CDS sequences from NCBI RefSeq for a target species
Orquesta analisis semantico del vault (conceptos, grafo, embeddings y busqueda) con procesamiento por lotes y manejo de errores.
Statistical genetics toolkit for fine-mapping (SuSiE), LD score regression (LDSC), and TWAS simulation, with support for GWAS summary statistics, heritability estimation, genetic correlations, and publication-ready reports
Diagnose and fix broken bone/blend shape/annotation mappings on 3D characters. Analyzes model data, compares against presets, extracts animation data, and generates corrected mappings. Use when annotations don't work, AUs don't animate correctly, or importing new character models. Primary focus on skeletal-only models like the Betta fish.
BindCraft protein binder design reference. Use when working with AF2 backpropagation, binder design, interface optimization, PyRosetta metrics, design filtering, or comparing with RFdiffusion approaches.
Trial Sequential Analysis for meta-analyses with information size calculations
单细胞分析最佳实践集合 - 100%完整覆盖（410个文件：407个HTML文档+3个项目文档）
Helps construct RwEq (rewrite equivalence) proofs using transitivity, congruence, and canonical lemmas from the LND_EQ-TRS system. Use when proving path equalities, working with quotients, or establishing rewrite equivalences in the ComputationalPaths library.
Spatial region-aware cell matching for CODEX/scRNAseq integration
Core bioinformatics concepts including SAM/BAM format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, and pairing issues.
Comprehensive skill for CellPhoneDB - Database of cell type markers and cell-cell communication analysis for single-cell data. Use for cell type annotation, ligand-receptor analysis, cell-cell interaction inference, and communication network visualization.
Advanced Maximum Likelihood phylogenetics with model selection (AIC/BIC), tree search algorithms (NNI/SPR/TBR), and performance optimization (Numba/GPU)
