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Coordinate complex bioinformatics pipelines across HPC and cloud environments with reproducible, containerized task graphs.
Adds the capability to design and deploy portable, containerized bioinformatics workflows using Nextflow DSL2. It allows agents to orchestrate multi-stage pipelines (e.g., RNA-seq from raw FASTQ to differential expression) while ensuring strict reproducibility and parameter traceability.
Use this skill when you need to manage a sequence of bioinformatics tools like FastQC, Salmon, edgeR, and limma across diverse compute environments (HPC, Cloud, Local). It is ideal for multi-omics integration requiring sequential preprocessing and analysis stages.
Scientific AI agents capable of shell execution and workflow management, such as those integrated with Claude Code or similar high-reasoning environments that can interface with HPC/Cloud CLI tools.
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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.
Metabolomics QC Report Generation
Automates the export of LC-MS metabolomics quality control results into publication-ready plots, HTML reports, and data tables.
Proteomics Spectral Quality Assurance
Validate Orbitrap mass spectrometry data by verifying instrument metadata and quantifying fragment ion signal-to-noise ratios.
GNPS Molecular Network Metadata Organization
Fetch, extract, and standardize GNPS molecular networking job archives for NPLinker integration.
Metabolomic Feature Table Imputation
Replace zero and missing values in LC-MS metabolomics feature tables using minimum-value-based interpolation.
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
Azure Impact Reporting — Integration & Troubleshooting
Guidance for configuring, troubleshooting, and integrating Azure Impact Reporting with Monitor, Logic Apps, Service Health and HPC guest health APIs.
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.