AIPOCH

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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Turns your protocol and analysis workflow into publication-ready Methods text. Use when writing or revising the Methods section of a biomedical manuscript, ensuring it complies with reporting guidelines (CONSORT, STROBE, PRISMA, TRIPOD), matches what is in the Results section, and satisfies journal-specific word limits and declarations. Also triggers on "write my methods", "revise my methods section", "how to report my statistics", "what do I need to include in methods for [study type]", or "make my methods CONSORT-compliant".

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Writes Specific Aims pages for grant applications. Use when drafting or revising the Specific Aims page (NIH R01/R21/R03), NSF Project Summary, or equivalent for any major funding agency. Also triggers on "write my specific aims", "help me draft specific aims for NIH", "what should a specific aims page include", "NSF project summary", "write my grant aims", or "how do I structure an R01".

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Acknowledges limitations in sample, design, measurement, and validation in a professional way that improves credibility without undermining the whole paper. Use when writing the limitations paragraph of a Discussion section, preparing a grant risk assessment, responding to reviewers about study weaknesses, or framing scope boundaries for a paper. Also triggers on "write my limitations", "how should I address the limitation of", "reviewer said my sample is too small", or "help me word this limitation".

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Rewrites technical research content into a structured lay summary that cross-disciplinary teams can quickly understand and act on. Use when the user wants to explain research to colleagues outside their specialty — clinicians, wet-lab scientists, bioinformaticians, product managers, or leadership. Trigger on: "lay summary", "explain my research to the team", "non-technical summary", "cross-disciplinary summary", "translate my findings", "align our team on the study", or any request to communicate research goals, findings, or next steps to a mixed or non-specialist audience. Part of the AIPOCH Academic Writing skill hub. Sits midstream: after research content is clarified, before downstream deliverables like slide decks or graphical abstracts.

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Condenses a full study into conference-submission abstract format. Use when adapting a manuscript abstract or study summary to meet a specific conference's word limit, structured format (Background/Methods/Results/Conclusion), character limits, or required section headings. Also triggers on "adapt my abstract for [conference]", "shorten my abstract to 250 words", "reformat for ASCO/ASGCT/SfN/AACR", "I need a conference abstract", or "cut my abstract to fit the word limit".

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Converts existing manuscript content into LaTeX format aligned with a target journal, conference, or template while preserving manuscript meaning and structural integrity.

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Converts a biomedical study storyline into a graphical abstract and, when direct image capability is available, generates the graphical abstract directly; otherwise it falls back to prompts, Mermaid flowcharts, or designer-facing briefs.

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Writes the full Introduction section of a biomedical manuscript based on an approved or sufficiently clear study logic, while preserving evidence boundaries and introduction discipline.

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Structures research progress into focused and actionable slides for lab meetings or project reviews without inventing missing content.

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Composes a Discussion around key findings, mechanisms, clinical relevance, and limitations. Use when writing or improving a Discussion section for any biomedical manuscript — including interpreting results, connecting to prior literature, addressing unexpected findings, framing limitations, and writing the conclusion. Also triggers on "write my discussion", "help me discuss my findings", "how do I compare to prior studies", "write the limitations paragraph", or "draft a discussion for my paper".

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Drafts journal-ready cover letters for manuscript submission. Use when preparing a submission package, communicating the manuscript's contributions and journal fit to editors, or tailoring the novelty framing for a specific journal's scope. Also triggers on "write a cover letter for my paper", "draft a submission cover letter", "help me write to the editor", or "cover letter for [journal name]".

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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.

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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.

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

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Writes complete, publication-grade figure legends that can stand on their own. Use when writing or revising figure legends for any scientific figure — bar charts, line graphs, scatter plots, box plots, heatmaps, survival curves, flow cytometry plots, western blots, microscopy images, or schematic diagrams. Also triggers on "write a figure legend for", "help me describe this figure", "my figure needs a legend", "write Figure 1 legend", or "what should a figure legend include".

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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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Builds background-gap-objective logic for biomedical manuscript introductions with clear study positioning and disciplined narrative structure.

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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 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: differential expression testing, gene clustering heatmaps, single-cell clustering workflows.

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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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