Latest version:
https://blog.ugeneyun.cn/software/PlantNGSTools.manual.html
install.packages('devtools')
devtools::install_github('biomarble/PlantNGSTools')
| 用途 | 模块名 | 备注 |
|---|---|---|
| DEG analysis with replicates 有生物学重复的差异表达基因分析 |
DEGAnalysis_DESeq2 | DESeq2 |
| DEG analysis without replicates 没有生物学重复的差异表达基因分析 |
DEGAnalysis_EBSeq | EBSeq |
| Gene Ontology (GO) enrichment analysis GO 功能富集 |
GOEnrich | topGO |
| Gene Ontology (GO) enrichment analysis with eggNOG-Mapper annotation 基于eggNOG-Mapper注释的GO富集 |
GOEnrich_eggnog | topGO |
| Gene Ontology (GO) enrichment analysis with PANNZER2 annotation 基于PANNZER2注释的GO富集 |
GOEnrich_pannzer2 | topGO |
| Gene Ontology (GO) enrichment analysis with custom annotation 自主注释的GO富集 |
GOEnrich_customMapping GOEnrich_customTable |
topGO |
| KEGG Pathway enrichment analysis KEGG Pathway富集 |
KEGGenrich | - |
| KEGG Pathway enrichment analysis with Blastkoala annotation 基于BlastKOALA的KEGG Pathway富集 |
KEGGenrich_blastkoala | - |
| KEGG Pathway enrichment analysis with custom pathway annotation 基于自主注释的KEGG Pathway富集 |
KEGGenrich_customTable | - |
| DEG Volcano Plot 差异表达分析火山图 |
VolcanoPlot | ggplot2 |
| DEG MA Plot 差异表达分析MA图 |
MAPlot | ggplot2 |
| Bubble plot for KEGG enrichment KEGG富集气泡图 |
KEGGbubble | ggplot2 |
| Bubble plot for GO enrichment GO富集气泡图 |
GObubble | ggplot2 |
| Bar plot for secondary GO Terms GO二级节点1条形图 |
GOBar | ggplot2 |
| Trait statistics 表型常用统计量2 |
multiTraitStat | - |
| Trait plot 表型统计图3 |
multiTraitPlot | - |
| Expression matrix combining 表达量矩阵按组合并 |
matrixGroup | - |
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