RNA-seq downstream analysis

This is a shiny app for RNA-seq downstream analysis for Arabidopsis thaliana.

It can do the following analysis:

• Differetial gene analysis using DESeq2
• GO and KEGG enrichment analysis using clusterProfiler
• GSEA analysis using clusterProfiler

The only data you need provided is expression matrix.

I use read.table("data.txt",sep="\t",header = TRUE) to parse the data.

Geneid	treat1	tread2	untreat1	untreat2
AT1G01010	163	168	233	219
AT1G01020	289	304	390	451
AT1G01030	32	27	37	25
AT1G01040	1430	1350	1706	1593
AT1G01046	14	13	18	19
AT1G01050	1646	1637	1904	1823
AT1G01060	132	143	152	103
AT1G01070	28	30	31	16
AT1G01073	0	0	0	0

Requirement:

• R > 3.5.0
• R packages:
  • shiny
  • DESeq2
  • stringr
  • tidyr
  • ggplot2
  • plotly
  • shinythemes
  • clusterProfiler
  • org.At.tair.db

功能升级

• 修改界面, 以shinydashboard 作为主题
• 增加文件下载功能
• 增加更多的注释信息