Click here to redirect to IDEA website.
To run IDEA functionally at local machine, you must make sure that all the dependencies were well loaded; To check the packages, one can simply type
library("Packages for check")
To date, the current version(IDEA 1.0) is work well based on the following versions of dependencies
shiny (>= 0.12.2),
DESeq2 (>= 1.6.2),
shinyBS (<= 0.25),
shinysky (>= 0.1.2),
edgeR (>= 3.2.4),
NOISeq (>= 2.8.0),
samr (>= 2.0),
PoissonSeq (>= 1.1.2),
ggplot2 (>= 1.0.1),
FactoMineR (>= 1.27),
VennDiagram (>= 1.6.5),
rmarkdown (>= 0.2.53),
RobustRankAggreg (>= 1.1)
User should notice that , the latest shinyBS is incompatible with IDEA; you should install the former version (0.25) before IDEA was imported. This is because current shinyBS removed the ```
progressBar
devtools::install_github( "ebailey78/shinyBS")
Run Instruction
-------------
To run, clone repository into local path and run as a Shiny App <br/>
example: <br/>
Clone repository into local directory '/Document/IDEA' (so that ui.R locates as '/Document/IDEA/ui.R') <br/>
then run in R under work directory of '/Document' : <br/>
```
runApp("IDEA")
```
Environment
-------------
R version 3.1.1
Packages:
Shiny (0.10.2), ShinySky(0.1.2), shinyIncubator (3.2.4) and their dependencies <br/>
DESeq2 (1.6.2), edgeR (3.2.4), SAMseq (2.0), PoissonSeq (1.1.2), NOISeq (2.8.0) and their dependencies <br/>
ggplot2, reshape, plyr, scale, RColorBrewer and other packages needed in plotting
Documentation
-------------
First stable version released.
Developer Information
-------------
FAQ
-------------
During the analysis procedure, you may encounter the following question due to software or enviroment bugs; We summarized those questions and give some solution for bug fixing:
1. "Error : unrecognized fields specified in html_dependency: attachment" while clicks the download report button:
Answer: This error is mainly caused by Rstudio version; you can fixed it by upgrading your RStudio to the latest version.
### Developers:
Qi Zhao, [email protected] <br/>
Peng Nie, [email protected] <br/>
Rucheng Diao, [email protected] <br/>
Lichen Sun, [email protected] <br/>
Yi Shi, [email protected]
### Maintainer:
Qi Zhao, Peng Nie <br/>
Please feel free contact us. <br/>