aipoch/medical-research-skills - 10ページ

graphical-abstract-wizard

Generate graphical abstract layout recommendations based on paper abstracts.

原文の言語: 英語

gtars

A high-performance Rust toolkit (with Python bindings and a CLI) for genomic interval analysis; use it when you need fast overlap queries, coverage track generation, genomic tokenization for ML, reference sequence verification, or fragment processing.

原文の言語: 英語

heatmap-beautifier

Professional beautification tool for gene expression heatmaps, automatically adds clustering trees, color annotation tracks, and intelligently optimizes label layout.

原文の言語: 英語

lab-budget-forecaster

Use lab budget forecaster for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

原文の言語: 英語

lamindb

This skill is applicable when using LaminDB. LaminDB is an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR-compliant. It is suitable for managing biological datasets (scRNA-seq, spatial transcriptomics, flow…

原文の言語: 英語

lipinski-rule-filter

Filter compound libraries based on Lipinski's Rule of Five for drug-likeness.

原文の言語: 英語

matchms

Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows.

原文の言語: 英語

matplotlib

A low-level plotting library for comprehensive customization. Use when fine-grained control over every plot element is needed, creating new types of charts, or integrating into specific scientific workflows. Can export to PNG/PDF/SVG for publication. For…

原文の言語: 英語

mechanism-flowchart

Generates Mermaid flowchart code and visual diagrams for pathophysiological.

原文の言語: 英語

meta-baujat-plot

Generate Baujat plots for heterogeneity analysis. Identify studies that contribute most to the overall meta-analysis results and heterogeneity, helping discover potential outlier studies. Input meta-analysis data CSV, output Baujat plot PNG and contribution…

原文の言語: 英語

meta-criteria-generator

Generates scientifically sound inclusion and exclusion criteria for Meta-Analysis based on a given title or keywords. Use when user wants to design eligibility criteria for a systematic review or meta-analysis.

原文の言語: 英語

meta-feasibility-analyzer

Analyzes the feasibility of a proposed Meta-analysis topic by searching for existing Meta-analyses and Clinical Trials on PubMed/ClinicalTrials.gov. Use when you need to evaluate if a topic is viable for a new Meta-analysis.

原文の言語: 英語

meta-forest-binary-plot

Generate meta-analysis forest plots for binary classification data. Input is a CSV file containing study names, event counts and sample sizes for experimental and control groups. Output includes forest plot PNG and data table CSV.

原文の言語: 英語

meta-forest-continuous-plot

Generate forest plots for meta-analysis of continuous data. Input a CSV file containing study names, means, standard deviations, and sample sizes for experimental and control groups. Output forest plot PNG and data table CSV.

原文の言語: 英語

meta-forest-model-plot

Generate forest plots for meta-analysis of survival data. Input is a CSV file containing study names, HR and 95% confidence intervals, output forest plot PNG and data table CSV. Supports both R and Python scripts.

原文の言語: 英語

meta-funnel-plot

Generate Meta-analysis funnel plots and perform publication bias testing. Takes CSV file with Meta-analysis data as input, outputs funnel plot PNG, Egger test and Begg test results.

原文の言語: 英語

meta-picos-generator

Generates PI(E)COS structure (Population, Intervention, Comparator, Outcomes, Study Design) from Meta-analysis or study titles. Use when the user wants to extract these elements from a title.

原文の言語: 英語

meta-radial-plot

Generate radial plots (Radial Plot/Galbraith Plot) for heterogeneity analysis. Visually assess heterogeneity across studies by displaying the relationship between standardized effect sizes and precision. Input: Meta-analysis data in CSV format; Output: Radial…

原文の言語: 英語

meta-sensitivity-plot

Generate leave-one-out sensitivity analysis plots for meta-analysis. Input is a CSV file containing meta-analysis data; outputs are a sensitivity forest plot (PNG) and a sensitivity data table (CSV) showing pooled effect estimates after excluding each study…

原文の言語: 英語

meta-title-generator

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…

原文の言語: 英語

metabolomics-workbench-database

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.

原文の言語: 英語

metagenomic-krona-chart

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

原文の言語: 英語

motif-logo-generator

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

原文の言語: 英語

neoantigen-predictor

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

原文の言語: 英語

neuropixels-analysis

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…

原文の言語: 英語

outcome-extraction-for-clinical-trials

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…

原文の言語: 英語

phylogenetic-tree-styler

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

原文の言語: 英語

preclinical-pkpd-analyst

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

原文の言語: 英語

probast-quality-assessment-for-prediction-model-studies

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).

原文の言語: 英語

pseudotime-trajectory-viz

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

原文の言語: 英語

pyopenms-skill

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…

原文の言語: 英語

pysam

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.

原文の言語: 英語

quadas-c-assessment-for-diagnostic-accuracy-studies

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

原文の言語: 英語

quality-assessment

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.…

原文の言語: 英語

quapas-quality-assessment-for-prognosis-studies

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.

原文の言語: 英語

rowan

Cloud-based quantum chemistry platform providing a Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformational search, molecular property calculations, protein-ligand docking (AutoDock Vina), and…

原文の言語: 英語

sanger-chromatogram-qa

Use sanger chromatogram qa for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

原文の言語: 英語

scanpy

Standard single-cell RNA-seq analysis pipeline. For quality control (QC), normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression analysis, and visualization. Best suited for exploratory single-cell transcriptomics…

原文の言語: 英語

scikit-bio

A Python bioinformatics toolkit for sequence, phylogeny, and microbiome/community-ecology analysis; use it when you need to compute diversity/ordination/statistics from biological data and standard formats (FASTA/FASTQ/Newick/BIOM).

原文の言語: 英語

scikit-survival

A comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival; use it when you need to model censored time-to-event outcomes, fit Cox/RSF/GB models or Survival SVMs, evaluate with C-index/Brier score, or handle…

原文の言語: 英語