README.md

In biomarble/PlantNGSTools: NGS bioinformatics tools for plants

PlantNGSTools - Plant RNA-seq analysis tool

Latest version:

Tutorial

https://blog.ugeneyun.cn/software/PlantNGSTools.manual.html

Installation

install.packages('devtools')
devtools::install_github('biomarble/PlantNGSTools')

Module

|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 analysisGO 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_customMappingGOEnrich_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 enrichmentKEGG富集气泡图|KEGGbubble|ggplot2| |Bubble plot for GO enrichmentGO富集气泡图|GObubble|ggplot2| |Bar plot for secondary GO TermsGO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|-|

Tips

• 任何疑问、提交Bug，请在Issues反馈

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biomarble/PlantNGSTools documentation built on Feb. 8, 2024, 2:46 a.m.