Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.
Medical Research Agent Skills is a library of agent instructions for medical and biomedical research, covering evidence analysis, study protocol design, data analysis, and academic writing. Researchers use it to guide compatible coding agents through common scientific workflows. The catalogue contains many of the library's skills and commands.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when filtering genes with high missingness and then imputing missing values in a bulk expression matrix with group-aware KNN through DMwR2, where donor samples are restricted by one annotation column before imputation. For strata with 10 or fewer samples, the script falls back to row-wise direct filling with mean…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when building a binary classification model from an expression matrix or other omics feature matrix with LASSO logistic regression, cross-validation, and coefficient path visualization. NOT for: multiclass classification, survival/Cox models, or ordinary linear regression.
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use this bioinformatics data analysis skill to construct a database-driven lncRNA-mRNA regulatory network from target lncRNA and/or gene lists by projecting shared miRNA evidence from local ceRNA reference tables. It does not infer networks from expression matrices.
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when assessing how well a survival model's predicted probabilities agree with observed outcomes by fitting a Cox model and generating bootstrap calibration curves at one or more prediction horizons from a clinical CSV file. NOT for: nomogram construction, univariate Cox screening, ROC analysis, or decision-curve…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when constructing a prognosis nomogram from survival-related clinical predictors, exporting the nomogram bundle and C-index table, and optionally rendering the final nomogram PDF. NOT for: univariate/multivariable Cox feature screening, calibration curves, ROC analysis, decision-curve analysis, or non-survival…
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when performing PCA principal component dimensionality reduction on tabular numeric data. Supports command-line parameter input, automatic numeric feature selection, parameter validation, result directory creation, and CSV or TXT format result export.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when you need a standardized R CLI workflow to build a protein-protein interaction network from a local gene list and an offline STRING cache, export node and edge tables, and render a reproducible PDF network plot. NOT for online API fetching, arbitrary graph databases, multi-omics integration, or non-STRING…
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when you need a standardized R CLI workflow to train a two-class random forest model from an expression-like feature matrix, rank variable importance, and generate reproducible error and importance plots. NOT for regression tasks, multi-class classification, missing-value imputation, preprocessing, or remote data…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when evaluating diagnostic biomarker performance from case-control expression data with logistic regression and ROC curves, exporting coefficient and AUC tables together with a ROC PDF. NOT for: survival analysis, time-to-event outcomes, multiclass classification, calibration curves, decision-curve analysis, or…
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when performing correlation analysis between two variables including Pearson and Spearman correlation methods. Supports command-line parameter input, automatic data format detection, parameter validation, result directory creation, and CSV or TXT format result export.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group, response status, subtype, or cohort labels. NOT for: gene network flow analysis, continuous-value trajectories, or graph-structured pathway visualization.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when estimating immune infiltration from bulk RNA-seq expression matrices with ssGSEA/GSVA, comparing case versus control groups, and generating downstream immune-score visualizations. NOT for single-cell RNA-seq, absolute cell proportion estimation, or clinical decision making.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when you need a standardized R CLI workflow to run two-class SVM-RFE feature ranking on an expression-like matrix, choose an informative feature count from cross-validated error, and generate reproducible ranking and error plots. NOT for regression, multi-class classification, missing-value imputation, or remote…
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when analyzing transcription factor (TF) regulatory networks using Dorothea database. Input gene list, identify regulating transcription factors, generate TF-Target network visualization. For: transcription factor enrichment analysis, gene regulatory network research.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when performing time-dependent ROC curve analysis for survival data with follow-up time, event status, and a numeric marker. Supports CSV/TXT/TSV/Excel input, riskscore as the default marker unless --markercol is provided, parameter validation, standardized output directories, AUC table export, ROC point export…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE coordinates and plots for group separation assessment. NOT for: differential expression testing, single-cell workflows requiring dedicated embeddings…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when running prognostic survival analysis on a clinical cohort with time-to-event data to estimate univariate and multivariable Cox proportional hazards models, export result tables, and generate forest plots. NOT for: nomogram construction, calibration curves, time-dependent ROC analysis, or model…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when building a weighted gene co-expression network from a bulk expression matrix and a sample group file, filtering variable genes by MAD, identifying co-expression modules with WGCNA, correlating modules with traits, and exporting module-level plots and gene tables. NOT for single-cell RNA-seq, differential…
aipoch/medical-research-skills
Skill Claude CodeCodex
Finds translational opportunities that connect basic-research discoveries to clinically meaningful use cases such as diagnosis, stratification, prognosis, treatment response prediction, monitoring, or therapeutic development. Use this skill when a user wants to turn a mechanism finding, pathway signal, cellular…
aipoch/medical-research-skills
Skill Claude CodeCodex
Identifies translationally meaningful paths for bioinformatics findings by mapping omics or computational discoveries to diagnosis, stratification, prognosis, treatment-response, monitoring, or target-nomination use cases, while auditing bridge evidence, assayability, and validation burden. Use this skill when a user…
aipoch/medical-research-skills
Skill Claude CodeCodex
Scans the biomarker landscape of a disease area by biomarker type, clinical/research use case, evidence layer, validation status, and maturity level. Use this skill when a user wants a field-level biomarker evidence map rather than a generic literature summary. Always separate exploratory biomarkers from externally…
aipoch/medical-research-skills
Skill Claude CodeCodex
Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases. Use when a user needs to construct a MeSH-based Boolean query, design a systematic review search, expand a concept with synonyms, apply study-type or date filters, or adapt a query across multiple databases. Also triggers…
aipoch/medical-research-skills
Skill Claude CodeCodex
Clarifies a vague clinical or biomedical research idea into a structured, bounded, searchable, researchable, and testable question. Always use this skill whenever a user has an early-stage clinical or research thought, an over-broad topic, an ill-defined evidence question, or an unclear problem statement that must be…
aipoch/medical-research-skills
Skill Claude CodeCodex
Explains why studies on the same biomedical topic reach different or opposing conclusions by auditing differences in population, endpoint definition, sample source, assay or platform, study design, statistical model, adjustment strategy, validation chain, and bias control. It separates true contradiction from apparent…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: