research▌

### Scikit Learn - name: "scikit-learn" - description: "Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hy..." - allowed-tools: "Read Write Edit Bash"

### Torch Geometric - name: "torch-geometric" - description: "PyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets. Use when w..."

### Pdf - name: "pdf" - description: "Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rota..."

### Pymatgen - name: "pymatgen" - description: "Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science."

### Paper Lookup - name: "paper-lookup" - description: "Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, ..."

### Pymc - name: "pymc" - description: "Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference."

### Paperzilla - name: "paperzilla" - description: "Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper details, markdown-based summaries, reco..."

### Protocolsio Integration - name: "protocolsio-integration" - description: "Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and..."

### Pathway Enrichment - name: "pathway-enrichment" - description: "Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanp..."

### Phylogenetics - name: "phylogenetics" - description: "Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial g..."