aipoch/medical-research-skills
Skill Claude CodeCodex
Checks biomedical manuscripts against reporting guidelines such as CONSORT, STROBE, PRISMA, and TRIPOD to identify missing or weak reporting elements before submission or revision.
aipoch/medical-research-skills
Skill Claude CodeCodex
Organizes biomedical figures, analyses, and result blocks into a clear Results section structure with disciplined narrative ordering and evidence-aware presentation.
aipoch/medical-research-skills
Skill Claude CodeCodex
Writes the full Results section of a biomedical manuscript from a sufficiently clear result structure, figure inventory, or analysis summary while preserving evidence boundaries and result hierarchy.
aipoch/medical-research-skills
Skill Claude CodeCodex
Builds prioritized manuscript revision plans for major or minor revisions by separating comments that require experiments, analyses, clarification, restructuring, or wording changes.
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
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
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
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
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
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
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
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.