AIPOCH

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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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 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, or single-cell data.

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Scrum-inspired paper review, revision, and R&R workflow. Handles docx/tex/md/PDF in English or Chinese. Auto-detects manuscript stage, estimates sprint count, runs multi-lens review (Contribution/Rigor/Writing/Editor), generates prioritized revision backlog, exports MD/DOCX/PDF/HTML reports. Use when asked to review a paper, revise based on reviewer comments, handle R&R, respond to peer review, plan paper revision sprints, or when user types /ps or /papersprint.

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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, tumor microenvironment score. NOT for: immune cell deconvolution, single-cell analysis, differential expression, clinical diagnosis.

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Improves medical English precision without changing the underlying facts, evidence boundaries, or intended scientific meaning.

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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, lambda.min, lambda.1se. NOT for: survival/Cox modeling, multiclass outcomes, single-cell data, or non-expression tables.

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Checks consistency across title, abstract, methods, results, figures, tables, and supplements to identify internal contradictions and version drift in biomedical manuscripts.

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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.

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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 single-cell RNA-seq, multi-group contrasts, count-model workflows such as DESeq2/edgeR, or non-expression omics data.

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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 time-to-event outcomes.

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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.

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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 list.

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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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Run a submission-readiness preflight on a manuscript before arXiv upload. Use when the user is preparing an arXiv submission, asks to check a paper before uploading, mentions hallucinated or fake references, leftover LLM meta-comments / prompts in text, placeholder data (TODO, TBD, XX%), AI-use disclosure, scholarly integrity, research integrity, or arXiv moderation risk — even if they don't say "preflight". Also trigger on phrases like "check my paper before arXiv", "verify my references", "scan for AI artifacts", "scan for LLM residue", "is my submission ready", or "review .tex/.bib before submit".

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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 biological groups.

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Optimizes manuscript titles and abstracts for information density, factual accuracy, and submission fit in biomedical research writing.

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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 paper", "which journal is best for my study", "find journals for my manuscript", "is this a good fit for [journal]", or "I need a journal with IF around X".

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Converts biomedical table content into clear manuscript or presentation narrative by prioritizing meaningful patterns, contrasts, and interpretation boundaries rather than restating every number.

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Organizes biomedical figures, analyses, and result blocks into a clear Results section structure with disciplined narrative ordering and evidence-aware presentation.

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Checks biomedical manuscripts against reporting guidelines such as CONSORT, STROBE, PRISMA, and TRIPOD to identify missing or weak reporting elements before submission or revision.

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Checks whether manuscript references are accurately matched to claims, appropriately scoped, and not overextended, misquoted, or second-hand cited.

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Reorganizes a paper into a storyline suitable for scientific posters. Use when planning the section structure, title hierarchy, figure selection, and live-explanation flow for an academic conference poster. Also triggers on "help me design a poster layout", "what sections should my poster have", "how do I arrange my poster", "poster structure for [conference]", or "which figures should I use for my poster".

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