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Differential Gene Expression Analysis (RNA-seq)

Name: Differential Gene Expression Analysis (RNA-seq)
Author: kenthompson2088

作者 kenthompson2088 · GitHub ↗ · v1.0.2 · MIT-0

cross-platform ⚠ suspicious

156

总下载

当前安装

版本数

在 OpenClaw 中安装

/install differential-gene-analysis-rna-seq

功能描述

Performs differential gene expression analysis on RNA-seq count data using DESeq2, generating significant gene lists and visualizations.

使用说明 (SKILL.md)

Differential Gene Expression Analysis (RNA-seq)\r

OpenCLAW Skill for bioinformatics data analysis.\r \r

License\r

MIT-0\r \r

Description\r

This skill performs differential gene analysis using DESeq2 with simulated expression data.\r \r

Input\r

input/count_matrix.csv\r \r

Output\r

output/volcano.png\r
output/pca.png\r
output/heatmap.png\r
output/diff_genes_significant.csv\r \r

Code\r

# ==============================\r
# OpenCLAW Skill Run Code\r
# ==============================\r
\r
if (!require("BiocManager", quietly = TRUE)) {\r
  install.packages("BiocManager", repos = "https://cloud.r-project.org/")\r
}\r
\r
BiocManager::install(c("DESeq2", "ggplot2", "pheatmap"), update = FALSE, ask = FALSE)\r
\r
library(DESeq2)\r
library(ggplot2)\r
library(pheatmap)\r
\r
if (!dir.exists("output")) dir.create("output")\r
\r
# Read input\r
count_df \x3C- read.csv("input/count_matrix.csv", row.names = 1)\r
count_matrix \x3C- as.matrix(count_df)\r
group \x3C- factor(c("Control","Control","Control","Treat","Treat","Treat"))\r
colData \x3C- data.frame(group = group)\r
\r
# DESeq2\r
dds \x3C- DESeqDataSetFromMatrix(round(count_matrix), colData, ~ group)\r
dds \x3C- dds[rowSums(counts(dds)) > 3, ]\r
dds \x3C- DESeq(dds)\r
res \x3C- results(dds, contrast = c("group", "Treat", "Control"))\r
res_sig \x3C- subset(res, padj \x3C 0.05 & abs(log2FoldChange) > 1)\r
write.csv(as.data.frame(res_sig), "output/diff_genes_significant.csv")\r
\r
# Volcano\r
res_df \x3C- as.data.frame(res)\r
res_df$sig \x3C- ifelse(res_df$padj \x3C 0.05 & abs(res_df$log2FoldChange) > 1, "Sig", "NS")\r
p \x3C- ggplot(res_df, aes(log2FoldChange, -log10(padj))) + geom_point(aes(color=sig)) + theme_bw()\r
ggsave("output/volcano.png", p, dpi=300)\r
\r
# PCA\r
vsd \x3C- vst(dds, blind=FALSE)\r
p_pca \x3C- plotPCA(vsd, intgroup="group") + theme_bw()\r
ggsave("output/pca.png", p_pca)\r
\r
# Heatmap\r
if(nrow(res_sig) > 0) {\r
  top \x3C- head(rownames(res_sig), 10)\r
  mat \x3C- t(scale(t(assay(vsd)[top,])))\r
  png("output/heatmap.png", width=800, height=600)\r
  pheatmap(mat, annotation_col=data.frame(group))\r
  dev.off()\r
}\r
\r
cat("✅ Skill run successfully\
")

安全使用建议

This skill appears to do what it says (DESeq2 analysis) but has several practical inconsistencies you should address before running: (1) The manifest (skill.json) references main.R and an R runtime while the bundle only contains SKILL.md with embedded R — update the manifest or provide the entry file so execution is deterministic. (2) input/count_matrix.csv in the package is empty; provide a properly formatted count matrix (rows=genes, columns=samples) that matches the hard-coded group factor (3 Control / 3 Treat) or modify the code to accept arbitrary sample groups. (3) The skill installs R/Bioconductor packages at runtime; that requires network access and will execute code downloaded from CRAN/Bioconductor — run in a sandboxed environment or pre-install/verify packages if you have security concerns. (4) If you need provenance, request the author/source (homepage) because the skill's source is unknown. If you plan to run this in a production environment, verify the input format, update the metadata, and consider pinning package versions to reduce variability.

功能分析

Type: OpenClaw Skill Name: differential-gene-analysis-rna-seq Version: 1.0.2 The skill performs standard bioinformatics differential gene expression analysis using the DESeq2 R package. The code in skill.md reads a local input file (count_matrix.csv), processes it using well-known libraries (DESeq2, ggplot2, pheatmap), and saves the resulting plots and data to an output directory. There are no indicators of data exfiltration, malicious command execution, or prompt injection.

能力评估

ℹ Purpose & Capability

The R code in SKILL.md implements differential gene expression using DESeq2, PCA, volcano, and heatmap which aligns with the skill's description. However, skill.json claims an entryFile (main.R) and runtime (R-4.2) while no such file exists in the bundle and the registry metadata earlier listed no required binaries—this metadata mismatch is inconsistent and may cause runtime confusion.

✓ Instruction Scope

The instructions are narrowly scoped to reading input/count_matrix.csv, running DESeq2-based analysis, creating plots, and writing outputs to output/. The code does not read unrelated system files, environment variables, or call external endpoints except to install R packages. The analysis uses a hard-coded sample grouping (3 Control / 3 Treat), which may not match user data.

ℹ Install Mechanism

The SKILL.md performs runtime package installation via install.packages('BiocManager', ...) and BiocManager::install(...). This installs from CRAN/Bioconductor (cloud.r-project.org and Bioconductor), which is a standard source for R packages but implies network access and the ability to execute newly downloaded code at runtime. There is no separate install spec in the manifest to declare or prepare these dependencies.

✓ Credentials

The skill requests no environment variables, no credentials, and no config paths. The lack of requested secrets is appropriate for its purpose.

✓ Persistence & Privilege

The skill is not always-enabled and uses normal, user-invocable settings. It does not request persistent agent privileges or modify other skills' configurations.

如何使用

确保已安装 OpenClaw（本地或 Docker 部署）
在对话框中输入安装命令：/install differential-gene-analysis-rna-seq
安装完成后，直接呼叫该 Skill 的名称或使用 /differential-gene-analysis-rna-seq 触发
根据 Skill 的参数说明提供必要输入，即可获得结构化输出

版本历史

v1.0.2

- Removed unnecessary file: plain.txt. - No changes to input, output, or core functionality.

v1.0.0

Initial release of the Differential Gene Analysis Skill for RNA-seq data. - Reads gene expression count matrices from CSV files. - Performs differential expression analysis using DESeq2. - Generates volcano, PCA, and heatmap plots. - Outputs a list of significant differentially expressed genes.

元数据

Slug differential-gene-analysis-rna-seq

版本 1.0.2

许可证 MIT-0

累计安装 0

当前安装数 0

历史版本数 2

常见问题