TuYv/ccpm - 第 11 页

gokegg-analysis

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.

原文语言：英语

grant-specific-aims-writer

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…

原文语言：英语

graphical-abstract-generator

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.

原文语言：英语

gsea

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

原文语言：英语

gsva-analysis-and-visualization

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…

原文语言：英语

hierarchical-clustering-plot

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…

原文语言：英语

immune-pathway-analysis

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.

原文语言：英语

introduction-logic-builder

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

原文语言：英语

introduction-section-writer

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.

原文语言：英语

km-survival-curve

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,…

原文语言：英语

knn-imputation

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,…

原文语言：英语

lasso-logistics-analysis

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…

原文语言：英语

latex-manuscript-format-converter

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

原文语言：英语

lay-summary-for-cross-disciplinary-teams

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,…

原文语言：英语

lightgbm-analysis

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

原文语言：英语

limitation-and-risk-writer

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,…

原文语言：英语

lncrna-regulatory-network-construction-analysis

Use this bioinformatics data analysis skill to construct a database-driven lncRNA-mRNA regulatory network from target lncRNA and/or gene lists by projecting shared miRNA evidence from local ceRNA reference tables. It does not infer networks from expression…

原文语言：英语

medical-english-precision-editor

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

原文语言：英语

methods-section-writer

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…

原文语言：英语

model-calibration-curve

Use when assessing how well a survival model's predicted probabilities agree with observed outcomes by fitting a Cox model and generating bootstrap calibration curves at one or more prediction horizons from a clinical CSV file. NOT for: nomogram construction,…

原文语言：英语

nomogram-construction

Use when constructing a prognosis nomogram from survival-related clinical predictors, exporting the nomogram bundle and C-index table, and optionally rendering the final nomogram PDF. NOT for: univariate/multivariable Cox feature screening, calibration…

原文语言：英语

paper-sprint-review

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,…

原文语言：英语

pca-dimensionality-reduction

Use when performing PCA principal component dimensionality reduction on tabular numeric data. Supports command-line parameter input, automatic numeric feature selection, parameter validation, result directory creation, and CSV or TXT format result export.

原文语言：英语

poster-storyline-builder

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",…

原文语言：英语

ppi-network-analysis

Use when you need a standardized R CLI workflow to build a protein-protein interaction network from a local gene list and an offline STRING cache, export node and edge tables, and render a reproducible PDF network plot. NOT for online API fetching, arbitrary…

原文语言：英语

reference-integrity-checker

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

原文语言：英语

reporting-guideline-compliance-checker

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

原文语言：英语

results-section-structurer

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

原文语言：英语

results-section-writer

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.

原文语言：英语

revision-strategy-planner

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

原文语言：英语

rf-model-importance-analysis

Use when you need a standardized R CLI workflow to train a two-class random forest model from an expression-like feature matrix, rank variable importance, and generate reproducible error and importance plots. NOT for regression tasks, multi-class…

原文语言：英语

roc-diagnostic-performance

Use when evaluating diagnostic biomarker performance from case-control expression data with logistic regression and ROC curves, exporting coefficient and AUC tables together with a ROC PDF. NOT for: survival analysis, time-to-event outcomes, multiclass…

原文语言：英语

sample-correlation-analysis

Use when performing correlation analysis between two variables including Pearson and Spearman correlation methods. Supports command-line parameter input, automatic data format detection, parameter validation, result directory creation, and CSV or TXT format…

原文语言：英语

sample-group-sankey-plot

Use when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group, response status, subtype, or cohort labels. NOT for: gene network flow analysis, continuous-value…

原文语言：英语

slide-deck-for-lab-meeting

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

原文语言：英语

ssgsea-immune-infiltration-analysis

Use when estimating immune infiltration from bulk RNA-seq expression matrices with ssGSEA/GSVA, comparing case versus control groups, and generating downstream immune-score visualizations. NOT for single-cell RNA-seq, absolute cell proportion estimation, or…

原文语言：英语

svm-model-importance-analysis

Use when you need a standardized R CLI workflow to run two-class SVM-RFE feature ranking on an expression-like matrix, choose an informative feature count from cross-validated error, and generate reproducible ranking and error plots. NOT for regression,…

原文语言：英语

table-narrative-writer

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

原文语言：英语

target-journal-matcher

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…

原文语言：英语

title-and-abstract-optimizer

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

原文语言：英语