research▌

### Pydeseq2 - name: "pydeseq2" - description: "Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis."

### Omero Integration - name: "omero-integration" - description: "Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows."

### Neuropixels Analysis - name: "neuropixels-analysis" - description: "Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuro..."

### Lamindb - name: "lamindb" - description: "This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRN..."

### Deepchem - name: "deepchem" - description: "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 be..." - allowed-tools: "Read Write Edit Bash"

### Flowio - name: "flowio" - description: "Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing."

### Cobrapy - name: "cobrapy" - description: "Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis." - allowed-tools: "Read Write Edit Bash"

### Clinical Decision Support - name: "clinical-decision-support" - description: "Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment ..." - allowed-tools: "Read Write Edit Bash"

### Get Available Resources - name: "get-available-resources" - description: "This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file wi..."

### Clinical Reports - name: "clinical-reports" - description: "Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP,..." - allowed-tools: "Read Write Edit Bash"