Click here to redirect to IDEA website.
To run IDEA functionally in local machine, you must make sure that all the dependencies were well installed. To check the dependencies, 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")
To install the latest development builds directly from GitHub, run this:(For some reason, we did not release the current version on CRAN or BIOCONDUCTOR site):
if (!require("devtools")) install.packages("devtools") devtools::install_github("likelet/IDEA")
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 process 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/>