Data & Analytics

Evaluates bias in medical literature (prognosis studies) using QUAPAS criteria. Use when the user wants to assess the quality or risk of bias of a medical paper text.

Automates critical appraisal and quality assessment for research papers by analyzing text against established methodological standards (such as risk of bias tools, quality checklists, or reporting guidelines) and synthesizing a structured evaluation report. Use when you need to assess the methodological quality, internal validity, or reporting completeness of any type of study—including RCTs, observational studies, systematic reviews, qualitative research, or diagnostic accuracy studies.

Automated bias assessment for diagnostic accuracy studies using QUADAS-C criteria. Requires full text input.

Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines.

Comprehensive tool for computational mass spectrometry using PyOpenMS; use when you need to read/write MS formats (mzML/mzXML/MGF), run signal processing (smoothing/peak picking), detect isotope features, or perform peptide identification in proteomics/metabolomics workflows.

Healthcare AI toolkit for clinical ML. EHR processing, clinical prediction (mortality, readmission, drug recommendation), medical coding (ICD/NDC/ATC), signals (EEG/ECG), datasets (MIMIC-III/IV, eICU, OMOP), and healthcare deep learning (RETAIN, SafeDrug, Transformer, GNN) via...

A Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when you need to read, write, or modify DICOM format medical imaging data, extract pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymize DICOM files,...

Differential gene expression analysis for bulk RNA-seq count matrices using a DESeq2-like workflow in Python; use when you need Wald tests, FDR correction, and optional LFC shrinkage for condition/batch/covariate designs.

Analyze data with `pseudotime-trajectory-viz` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

Classify clinical trial protocol deviations as major or minor based on ICH E6/GCP guidelines. Three-impact-dimension assessment (safety, data integrity, scientific validity), confidence scoring, and regulatory compliance reporting with recommended actions.

Assess bias in medical prediction model studies using PROBAST tool. Use when user wants to evaluate the quality or risk of bias of a medical paper (text or PDF).

Use preclinical pkpd analyst for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

Analyze data with `phylogenetic-tree-styler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

Use pathology roi selector for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

A full-featured computational pathology toolkit for advanced WSI analysis, including multiplexed immunofluorescence (CODEX, Vectra), nuclei segmentation, tissue graph construction, and machine learning model training on pathology data. Supports over 160 slide formats. For simp...

Use outlier detection handler for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

Clinical research outcome extraction for meta-analysis. Use when users need to extract outcome measures (binary, continuous, or survival data) from clinical research papers for systematic review and meta-analysis. Handles both database lookup by PMID and real-time LLM extraction.

End-to-end Neuropixels extracellular electrophysiology analysis (SpikeGLX/Open Ephys/NWB) including preprocessing, motion correction, Kilosort4 spike sorting, QC metrics, and Allen/IBL-style curation; use when processing Neuropixels recordings or when users mention Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, drift/motion correction, or unit curation.

Comprehensive biosignal processing for ECG/PPG/EEG/EDA/RSP/EMG/EOG; use when you need to clean, segment, and extract physiological features for HRV, event-related responses, complexity metrics, or multimodal psychophysiology pipelines.

Predict neoantigens that may be recognized by the immune system based.

Generate publication-quality sequence logos for DNA or protein motifs.

Analyze data with `metagenomic-krona-chart` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

Access NIH Metabolomics Workbench (4,200+ studies) via REST API. Query metabolites, RefMet nomenclature, MS/NMR data, m/z search, study metadata for metabolomics and biomarker discovery.

Generates Meta-Analysis research titles based on user keywords, utilizing PubMed search results if available, or creative generation otherwise. Use when the user wants to brainstorm or generate titles for a meta-analysis, specifically starting from keywords or a topic.