AIPOCH

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.

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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.

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Run GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.

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Turns reviewer comments into structured, professional point-by-point responses linked to manuscript revisions, clarifications, rebuttals, and additional analyses.

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Calibrates manuscript claim strength so wording matches the actual evidence level, study design, and validation status.

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Builds prioritized manuscript revision plans for major or minor revisions by separating comments that require experiments, analyses, clarification, restructuring, or wording changes.

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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, spatial data, clinical diagnosis, or workflows that require the original hosted CIBERSORT web service.

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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, single-cell analysis, methylation analysis, clinical diagnosis.

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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.

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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 or median. NOT for: single-cell data, multi-column stratification, non-tabular inputs, network access, or interactive workflows.

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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.

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Use when training a LightGBM model on tabular data in R and returning model metrics, feature importance ranking tables, and feature importance plots.

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