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
- 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