aipoch/medical-research-skills - Page 10

graphical-abstract-wizard

Generate graphical abstract layout recommendations based on paper abstracts.

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.

heatmap-beautifier

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

lab-budget-forecaster

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

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…

lipinski-rule-filter

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

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.

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…

mechanism-flowchart

Generates Mermaid flowchart code and visual diagrams for pathophysiological.

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…

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.

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.

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.

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.

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.

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.

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.

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…

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…

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…

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.

metagenomic-krona-chart

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

motif-logo-generator

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

neoantigen-predictor

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

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…

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…

phylogenetic-tree-styler

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

preclinical-pkpd-analyst

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

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).

pseudotime-trajectory-viz

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

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…

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.

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

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

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.…

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.

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…

sanger-chromatogram-qa

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

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…

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).

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…