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Install and run the BD Rhapsody™ Sequence Analysis Pipeline (v3.0) on a shared cluster or remote Linux server with no root and no container runtime. Covers the self-contained install bundle, reference archives, FASTQ manifests, per-library YML generation, SLURM array execution, outputs, sample-tag demultiplexing, and the failure modes that cost hours — wrong Sample_Tags_Version on nuclei runs, uncapped Maximum_Threads, node-local scratch, and pinning a stale `latest` bundle.
Advanced single-cell multi-omics analysis including scRNA-seq, scCITE-seq, scATAC-seq, and TARGET-seq. Use when analyzing single-cell data, cell type identification, trajectory analysis, differential expression, UMAP/clustering, integrating protein and RNA modalities (TotalVI), or working with Scanpy, Seurat, scvi-tools. Includes workflows for MPN, hematologic malignancies, megakaryocyte biology.
Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.
Basado en la clasificación ocupacional SOC
Mostrando SKILL.md
| name | chematagent-drug-discovery |
| description | Chemical Lab Agent |
| keywords | ["chemistry","drug-discovery","tools","synthesis","property-prediction"] |
| measurable_outcome | Plan a synthesis route and predict ADMET properties for a candidate molecule with >80% validity. |
| license | MIT |
| metadata | {"author":"CheMatAgent Team","version":"1.0.0"} |
| compatibility | [{"system":"Python 3.9+"}] |
| allowed-tools | ["run_shell_command","read_file"] |
A two-tiered agent system with access to 137 Python-wrapped chemical tools for drug discovery and materials science.
User: "Design a molecule similar to Aspirin but with higher solubility."
Agent Action:
python -m chematagent.design --scaffold "Aspirin" --objective "maximize solubility"