aipoch/medical-research-skills - Page 9

peer-review-response-drafter

Assist in drafting professional peer review response letters. Trigger.

peer-review

Conduct professional peer reviews for papers or theses, providing structured evaluations and improvement suggestions; use when you need a pre-submission assessment, an internal review, or academic quality control.

personal-statement

Use when writing medical school personal statements, residency application essays, fellowship statements, or graduate school admissions essays. Crafts compelling narratives highlighting clinical experiences, research achievements, and career motivations for…

poster-layout-planner

Use poster layout planner for other workflows that need structured execution, explicit assumptions, and clear output boundaries.

presentation-hook

Creates engaging opening statements and powerful closings for medical.

prior-auth-letter-drafter

Generate professional prior authorization request letters for insurance companies with proper clinical justification and formatting.

q-and-a-prep-partner

Predict challenging questions for presentations and prepare structured responses.

radiology-image-quiz

Use when creating radiology educational quizzes, preparing board exam questions, or studying medical imaging cases. Generates interactive quizzes with X-ray, CT, MRI, and ultrasound images for medical education.

recommendation-letter-assistant

Helps faculty and mentors draft standardized recommendation letters for.

reference-style-sync

One-click synchronization and standardization of reference formats in literature management tools, intelligently fixing metadata errors.

residency-interview-prep

Mock interview preparation tool for residency Match interviews. Generates.

semantic-consistency-auditor

Use semantic consistency auditor for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

tone-adjuster

Use when converting medical text between academic and patient-friendly tones, translating medical jargon for patients, adapting research papers for public audiences, or rewriting clinical notes for patient handouts. Maintains medical accuracy while adjusting…

usmle-case-generator

Generate USMLE Step 1/2 style clinical cases with patient history, physical.

visual-content-desc

Generates detailed text descriptions of medical images and charts for.

adme-property-predictor

Analyze data with `adme-property-predictor` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

anndata

Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.

baseline-extraction-for-clinical-trials

Extracts clinical trial baseline data (study, region, participants, etc.) from article text or PMID. Checks PubMed for metadata; always falls back to LLM extraction for full details.

biopython-advanced

Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.

biopython-alignment

Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.

biopython-phylo

Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.

biopython-sequence-io

Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O, lightweight sequence manipulation, or scalable processing of large sequence datasets.

biopython

A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.

biopython-structure

Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.

bioservices

Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially for cross-database analysis and identifier mapping.

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.

cnv-caller-plotter

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

cobrapy

Constraint-based reconstruction and analysis (COBRA) for metabolic models; use when you need to simulate growth/production, analyze flux ranges, or run knockout and medium studies from SBML/JSON/YAML models.

code-refactor-for-reproducibility

Use when refactoring research code for publication, adding documentation to existing analysis scripts, creating reproducible computational workflows, or preparing code for sharing with collaborators. Transforms research code into publication-ready,…

crispr-screen-analyzer

Process CRISPR screening data to identify essential genes and hit candidates. Performs quality control, statistical analysis (RRA), and hit calling for pooled CRISPR screens including viability screens and drug resistance/sensitivity studies.

deeptools

NGS analysis toolkit. Used for BAM to bigWig conversion, quality control (correlation, PCA, fingerprint plots), heatmaps/feature plots (TSS, peaks), suitable for ChIP-seq, RNA-seq, ATAC-seq visualization.

dnanexus-integration

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.

etetoolkit

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.

experimental-data-analysis

Statistical analysis and reporting for experimental datasets; use when you need to interpret experimental results, test significance (t-tests/ANOVA), or generate reproducible reports.

facs-gating-viz-style

Use facs gating viz style for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

fastqc-report-interpreter

Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.

flowio

Parse Flow Cytometry Standard (FCS) files v2.0–3.1 and extract events/metadata for preprocessing workflows (e.g., when you need NumPy arrays, channel info, or CSV/DataFrame export from cytometry files).

gene-structure-mapper

Use gene structure mapper for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

geniml

Machine learning toolkit for genomic interval (BED) data; use it when you need to tokenize BED collections and train embeddings for regions/cells/labels, build consensus peak universes, or run similarity search and downstream ML on chromatin accessibility…

geopandas

A Python library for reading, writing, and analyzing geospatial vector data; use it when you need spatial operations (buffer/overlay/join), CRS reprojection, or map visualization on formats like Shapefile/GeoJSON/GeoPackage or PostGIS.