MCP App StoreMCP App StoreThis skill provides a rigorous framework for performing quality control on cytometry data. It focuses on identifying and removing acquisition artifacts such as flow-rate instability, signal drift, and dead-cell contamination using specialized R packages.
Use this skill when processing raw cytometry data before downstream analysis. It is critical for ensuring data integrity before performing compensation, transformation, clustering, or differential analysis.
flowAI, PeacoQC, flowCut, and flowClean for anomaly detection.Primarily designed for agents with R execution capabilities or those assisting bioinformatics researchers using the Operon IDE.
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Seq Wrangler
Sequence data QC, trimming, alignment, and BAM processing pipeline helper — wraps FastQC, fastp/Trimmomatic, BWA/Bowtie2/Minimap2, and SAMtools for automated re
ToolUniverse Gateway
Unified agent gateway to 1000+ scientific tools (bioinformatics, drug discovery, genomics) via Harvard's ToolUniverse, returning JSON for downstream workflows.
MatchMS (mass spectrometry processing)
Mass spectrometry data processing: import/export mzML/MGF/MSP, filter and normalize spectra, compute spectral similarity (cosine/modified cosine), and build rep
KEGG Pathway Enrichment (clusterProfiler)
Run KEGG pathway and module enrichment using clusterProfiler (enrichKEGG/enrichMKEGG) to find metabolic and signaling pathways over-represented in a gene list.
Network Toxicology & Docking Research Planner
Generates four-tier network toxicology + molecular docking study designs (Lite → Publication+) with step-by-step workflows, validation strategies, figure plans,
Bizard — Biomedical Visualization Atlas
A comprehensive atlas of biomedical data visualization tutorials and examples (R/Python/Julia) that provides reproducible code and guidance for plots used in bi
Bismark Methylation Calling
Extract per-cytosine methylation calls (CpG/CHG/CHH) from Bismark-aligned BAMs and produce bedGraph/coverage reports for downstream analysis.
E.Copi — Scientific Multi-Agent System
Multi-expert scientific agent for drug discovery and biomedical research that instantiates domain specialists, integrates multimodal evidence, and generates ana