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
Structures research progress into focused and actionable slides for lab meetings or project reviews without inventing missing content.
aipoch/medical-research-skills
Skill Claude CodeCodex
Converts biomedical table content into clear manuscript or presentation narrative by prioritizing meaningful patterns, contrasts, and interpretation boundaries rather than restating every number.
aipoch/medical-research-skills
Skill Claude CodeCodex
Matches your study to appropriate journals based on topic, design, and evidence strength. Use when deciding where to submit a manuscript, comparing journal options by impact factor vs scope fit vs method tolerance, or finding a realistic submission target after a rejection. Also triggers on "where should I submit this…
aipoch/medical-research-skills
Skill Claude CodeCodex
Optimizes manuscript titles and abstracts for information density, factual accuracy, and submission fit in biomedical research writing.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when training a LightGBM model on tabular data in R and returning model metrics, feature importance ranking tables, and feature importance plots.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when building XGBoost models on tabular data and returning feature importance ranking outputs. Supports binary classification and regression with automatic task detection, train-test split, performance tables, feature importance ranking tables, and PNG importance plots.
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when correcting batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and generating before-and-after QC plots. NOT for: single-cell integration, raw FASTQ processing, differential expression without batch labels, or datasets without…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports and PDF visualization in a single output directory. NOT for: differential expression, single-cell analysis, enrichment analysis, or workflows without a key gene…
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when estimating relative immune cell infiltration from a bulk expression matrix with a CIBERSORT-style nu-SVR deconvolution workflow based on an LM22 signature matrix, comparing one case group against one control group, and generating structured tables plus immune-fraction plots. NOT for single-cell RNA-seq…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization. NOT for: differential expression analysis, single-cell clustering workflows, or non-expression tables.
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when evaluating the clinical utility of a binary prediction model from a single clinical CSV file by fitting a logistic decision-curve model, plotting decision and clinical-impact curves, and exporting summary outputs. NOT for: survival calibration, ROC-only discrimination analysis, nomogram construction, or…
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when building a decision tree model in R and generating feature importance ranking outputs. Supports classification and regression, automatic task detection, parameter validation, model evaluation summaries, and exports of feature-importance tables and figures.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap. Triggers include DEG analysis, volcano plot, clustered heatmap, limma-based two-group comparison, and case-vs-control screening. NOT for…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and heatmap visualization. NOT for:single-cell RNA-seq, methylation analysis, non-expression data.
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when selecting predictive genes or other molecular features from bulk expression matrices for binary case-vs-control classification with elastic net logistic regression, including coefficient path and cross-validation plots. Trigger keywords: elastic net, glmnet, feature selection, binary classification…
aipoch/medical-research-skills
Skill Claude CodeCodex
Use this skill to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally generate group-wise ESTIMATE score boxplots plus significance tables when a sample group file is supplied. Trigger keywords: ESTIMATE, immune score, stromal score…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when validating an existing prognostic risk signature on an external bulk expression cohort with survival outcomes, producing risk scores, Kaplan-Meier curves, risk distribution plots, heatmap, and time-dependent ROC curves. NOT for: model training, feature selection, nomogram construction, calibration analysis…
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory analysis. NOT for count-model normalization such as TPM/DESeq2 size factors, batch correction, or single-cell preprocessing.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart. NOT for single-cell RNA-seq, methylation data, or non-expression data.
aipoch/medical-research-skills
Skill Claude CodeCodex
Run GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use this skill to run GSVA or ssGSEA pathway-level differential analysis from a bulk expression matrix and a sample group file, then generate a heatmap from the saved GSVA result object. Trigger keywords: GSVA, ssGSEA, pathway enrichment, KEGG pathway analysis, MSigDB. NOT for: gene-level differential expression…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Use when building a sample-level hierarchical clustering dendrogram from a bulk expression matrix and sample annotation table, especially for QC, batch inspection, or sample similarity assessment. Trigger keywords: hierarchical clustering, dendrogram, sample QC, batch inspection, sample similarity. NOT for…
aipoch/medical-research-skills
Skill Claude CodeCodex needs its repo
Run immune pathway GSVA or ssGSEA analysis from a bulk expression matrix, a sample group file, and a local immune Reactome gene-set table, then export differential pathway results and a heatmap for two-group comparison.
aipoch/medical-research-skills
Skill Claude CodeCodex
Use when generating Kaplan-Meier survival curves from tabular survival data containing time, event status, and a precomputed risk group. Supports command-line parameter input, parameter validation, automatic time-unit handling, single-file PDF figure export, and session metadata capture.
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: