AI prompts and agent skills.

By nealcarenOriginal project

MIT · FreeView skill

SkillData & Analytics

differential-abundance

Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

ggplot2 Fundamentals

Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts. Use when creating static figures for papers, presentations, or reports in R.

✳Claude Code>_Codex◈OpenClaw+1

Academic Writer Researcher

By David-Li0406Original project

Apache-2.0 · FreeView skill

SkillEducation & Research

Format Citations

Format citations across academic styles (APA 7, Chicago, Vancouver, IEEE) using CSL processors and R tooling. Convert between citation styles, generate in-text citations and reference lists, and validate formatting against style guides using citeproc, knitcitations, and Quarto's built-in citation...

◈OpenClaw

By pjt222Original project

MIT · FreeView skill

SkillData & Analytics

Manage Bibliography

Create, merge, and deduplicate BibTeX bibliography files using R packages (RefManageR, bibtex). Parse .bib files into structured R objects, merge multiple bibliographies with deduplication by DOI or title similarity, generate entries from DOI/ISBN/arXiv ID, and export clean sorted .bib files. Use...

✳Claude Code>_Codex◈OpenClaw+1

By pjt222Original project

MIT · FreeView skill

SkillData & Analytics

Generate Statistical Tables

Generates publication-ready statistical tables using R for descriptive statistics, regression results, and APA formatting.

◈OpenClaw

Data Scientist Researcher

By pjt222Original project

MIT · FreeView skill

SkillData & Analytics

Reproducible Research with R

Create reproducible research workflows with R and RMarkdown/Quarto

◈OpenClaw

By wentoraiOriginal project

MIT · FreeView skill

SkillData & Analytics

Decision Curve Analysis

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 ...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Time-Dependent ROC Analysis

Use when performing time-dependent ROC curve analysis for survival data with follow-up time, event status, and a numeric marker. Supports CSV/TXT/TSV/Excel input, `risk_score` as the default marker unless `--marker_col` is provided, parameter validation, standardized output directories, AUC table...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Batch Effect Correction

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 data...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Gene Protein Expression Matrix Normalization

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.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Differential Expression Analysis

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.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

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 classification, calibration curves, decision...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

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, univariate Cox screening, ROC analysi...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Differential Expression Gene Screening Analysis (Volcano Plot & Clustered Heatmap)

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 s...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

ESTIMATE Immune Score Analysis

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...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Consensus Clustering Analysis

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.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

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 analysis, MSigDB. NOT for: gene-level differe...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Volcano Plot Script Generator

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expression data, p-value vs fold-change scatter plots, publication-ready figures for bioinformatics analysis.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

Univariate and Multivariable Cox Regression

Use when running prognostic survival analysis on a clinical cohort with time-to-event data to estimate univariate and multivariable Cox proportional hazards models, export result tables, and generate forest plots. NOT for: nomogram construction, calibration curves, time-dependent ROC analysis, or...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

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.

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

External Model Validation

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, c...

◈OpenClaw

By aipochOriginal project

MIT · FreeView skill

SkillData & Analytics

MOFA2 Integration

Discovers shared and view-specific latent factors across bulk multi-omics blocks (RNA-seq, proteomics, methylation) on a common sample axis with MOFA2's unsupervised Bayesian group factor model, then attributes per-view variance explained and interprets signed factor weights. Covers why a factor ...

✳Claude Code>_Codex◈OpenClaw+1

By GPTomicsOriginal project

MIT · FreeView skill

SkillData & Analytics

Genomic SEM

Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles res...

✳Claude Code>_Codex◈OpenClaw+1