Explore skills

This skill orchestrates end-to-end bulk RNA-seq analysis, processing raw FASTQ reads through QC, trimming, alignment, and quantification to assemble a gene-level counts matrix. It then performs differential expression, pathway enrichment, and generates publication-ready figures.

This skill is for machine learning tasks involving genomic interval data (BED files), such as training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), or building consensus peaks. It applies to BED file collections, scATAC-seq data, and chromatin accessibility datasets.

Search scientific papers and retrieve structured experimental data from full-text studies via the BGPT MCP server. It returns over 25 fields per paper, including methods, results, and conclusions, useful for literature reviews and finding experimental details beyond abstracts.

Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation, including photos, illustrations, artwork, and concept art, but not technical diagrams. For technical diagrams, use the scientific-schematics skill.

This skill detects and reports available system resources (CPU cores, GPUs, memory, disk space) at the start of computationally intensive scientific tasks. It generates a JSON file with resource information and strategic recommendations to guide computational approach decisions, such as using parallel processing or out-of-core computing.

This tool provides lightweight WSI tile extraction and preprocessing, ideal for basic slide processing, tissue detection, and stain normalization for H&E images. It's best suited for simple pipelines, dataset preparation, and quick tile-based analysis, with pathml recommended for advanced applications.

Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.

This skill analyzes Neuropixels neural recordings, covering SpikeGLX/OpenEphys data loading, preprocessing, motion correction, Kilosort4 spike sorting, quality metrics, and AI-assisted visual analysis for Neuropixels 1.0/2.0 extracellular electrophysiology.

This operator toolkit supports nf-core/pacsomatic matched tumor-normal workflows from BAM inputs, enabling validation, samplesheet generation, Nextflow launch artifact preparation, local or scheduler-based execution, and failure triage. It triggers on requests to run pacsomatic or prepare launch commands.

Phylogenetic tree toolkit (ETE) for phylogenomics, offering tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy integration, and visualization (PDF/SVG).

Cheminformatics toolkit for fine-grained molecular control, supporting SMILES/SDF parsing, descriptors, fingerprints, substructure search, 2D/3D generation, similarity, and reactions. For standard workflows with a simpler interface, use datamol (a wrapper around RDKit); for advanced control, custom sanitization, or specialized algorithms, use rdkit directly.

Genomic file toolkit for NGS data processing pipelines. It reads/writes SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extracts regions, and calculates coverage.