medical-research-skills

meta-analysis-forest-plotter

Use when creating forest plots for meta-analyses, visualizing effect sizes across studies, or generating publication-ready meta-analysis figures. Produces high-quality forest plots with confidence intervals, heterogeneity metrics, and subgroup analyses.

cnv-caller-plotter

Detect copy number variations from whole genome sequencing data and generate publication-quality genome-wide CNV plots. Supports CNV calling, segmentation, tumor-normal comparison, and BED format export for cancer genomics and rare disease analysis.

grant-gantt-chart-gen

Create project timeline visualizations for grant proposals

upset-plot-converter

Convert complex Venn diagrams with more than 4 sets into clearer UpSet plots for publication-ready set intersection visualization.

crispr-grna-designer

Design CRISPR gRNA sequences for specific gene exons with off-target prediction and efficiency scoring. Trigger when user needs gRNA design, CRISPR guide RNA selection, or genome editing target analysis.

microbiome-diversity-reporter

Interpret Alpha and Beta diversity metrics from 16S rRNA sequencing results and generate visualization reports for microbiome analysis.

gene-structure-mapper

Visualize gene structure with exon-intron diagrams, domain annotations, and mutation position markers. Produces SVG, PNG, or PDF figures suitable for publication from a gene symbol input.

ecrf-designer

Design clinical trial CRFs with proper validation rules

blockbuster-therapy-predictor

Predict which early-stage biotechnology platforms (PROTAC, mRNA, gene editing, etc.) have the highest potential to become blockbuster therapies. Analyzes clinical trial progression, patent landscape maturity, and venture capital funding trends to generate investment and R&D prioritization scores. Trigger when: User asks about technology investment potential, platform selection, or therapeutic modality comparison.

fastqc-report-interpreter

Interprets FastQC quality control reports for NGS data. Identifies quality issues, diagnoses root causes, and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq datasets.

neoantigen-predictor

Predict patient-specific neoantigen candidate peptides with high immunogenicity based on HLA typing and tumor mutation profiles, for tumor immunotherapy target screening.

citation-chasing-mapping

Use when identifying seminal papers in a research field, mapping research lineage and intellectual heritage, discovering related work through reference tracking, or finding potential collaborators through co-citation analysis. Maps citation networks to trace research evolution, identify influential papers, and discover hidden connections in scientific literature. Supports systematic reviews, bibliometric analysis, and research planning through comprehensive citation tracking.

nih-biosketch-builder

Generate NIH Biosketch documents compliant with the 2022 OMB-approved format

clinicaltrials-gov-parser

Monitor and summarize competitor clinical trial status changes from ClinicalTrials.gov. Trigger: When user asks to track clinical trials, monitor trial status changes, get updates on specific trials, or analyze competitor trial activities. Use cases: Pharma competitive intelligence, trial monitoring, status tracking, recruitment updates, completion alerts.

in-silico-perturbation-oracle

Virtual gene knockout simulation using foundation models to predict transcriptional changes

dpi-upscaler-checker

Check image DPI and intelligently upscale low-resolution images using super-resolution

abstract-summarizer

Transform lengthy academic papers into concise, structured 250-word abstracts capturing background, methods, results, and conclusions. Optimized for research papers, theses, and technical reports across scientific disciplines.

circos-plot-generator

Generate Circos configuration files for circular genomics data visualization. Supports genomic variations (SNPs, CNVs, structural variants), cell-cell communication networks, and custom track configurations for publication-ready circular plots. Generates configuration files only — rendering requires Circos installed separately.

graph-interpretation

Use when interpreting scientific graphs and charts, explaining data visualizations for research presentations, writing figure captions for publications, or analyzing trends in clinical research data. Converts complex visual data into clear, accurate explanations for academic papers, clinical reports, and public presentations.

phylogenetic-tree-styler

Beautify phylogenetic trees with taxonomy color blocks, bootstrap values, and timelines. Accepts Newick format and outputs PNG, PDF, or SVG.

citation-formatter

Use when formatting references for journal submission, converting between citation styles (APA, MLA, Vancouver, Chicago), generating bibliographies for manuscripts, or ensuring consistent reference formatting. Automatically formats citations and bibliographies in 1000+ academic styles. Ensures reference accuracy, completeness, and compliance with journal requirements. Supports batch conversion and integration with reference managers.

dei-statement-drafter

Draft Diversity, Equity, and Inclusion statements for academic applications

grant-budget-justification

Generate narrative budget justifications for NIH/NSF applications

adaptive-trial-simulator

Design and simulate adaptive clinical trials with interim analyses, sample size re-estimation, and early stopping rules. Evaluate Type I error control, power, and expected sample size via Monte Carlo simulation before trial initiation.

medical-cv-resume-builder

Generates US medical industry standard CVs and resumes.