MCP App StoreMCP App Store
from Agentic Science Builder Skill Collections15
Automates the export of LC-MS metabolomics quality control results into publication-ready plots, HTML reports, and data tables.
This skill enables an agent to package analyzed metabolomics quality control results from an mzQuality SummarizedExperiment object into a structured project directory. It generates high-quality visualizations and interactive HTML reports that categorize compounds by confidence levels (High Confidence, Caution, and Low SNR).
Use this skill after the doAnalysis process has been completed, including outlier detection, batch correction, and reliability filtering. It is ideal for communicating scientific results to non-R users or preparing data for publication.
createReports function, configuring summary and compound reports, and validating the output directory structure.mzQuality R package and the SummarizedExperiment framework.Designed for agents capable of executing R scripts or interacting with Bioconductor-based bioinformatics pipelines (e.g., specialized scientific AI agents, Claude Code with R environment).
This skill has not been reviewed by our automated audit pipeline yet.
GitHub Actions Workflow Inspector
Verify and locally reproduce GitHub Actions CI workflows to validate badge status and build integrity.
Injection Sequence Annotation
Identifies and validates QCpool sample spacing in Sciex Multiquant metabolomics/lipidomics exports.
PyTorch Pretrained Weight Loader
Load pretrained PyTorch model checkpoints to rank candidate molecules or score spectra in metabolomics without retraining.
Positional Encoding for Spectral Sequences
Embeds sequential information into mass spectrum m/z-intensity pairs for transformer-based MS/MS interpretation in IDSL_MINT.
Record Field Transformation & Collation
Transform and collate tabular records into structured JSON dictionaries using field mapping, filtering, and grouping for scientific metadata.
Fragmentation Spectrum Extraction
Extract and deconvolve individual fragmentation spectra from composite mass spectrometry data for metabolomics and exposomics annotation.
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
Quality Control Provisions (Trademark License Exhibit)
Drafts a trademark license exhibit establishing quality standards, inspection rights, sample approval procedures, remediation, and recall obligations to preserv
matchms — Mass Spectrometry Processing
Python library skill for importing, filtering, and comparing mass spectra (mzML/MGF/MSP); builds reproducible preprocessing pipelines and computes spectral simi
MatchMS — Mass Spectrometry Utilities
Import, process and compare mass spectrometry spectra (mzML/MGF/MSP) with filters, similarity metrics and reproducible pipelines for metabolomics workflows.
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,