Identification of differentially expressed genes is a major application of count data such as RNA-Seq. To this end, many tools such as DESeq (Anders and Huber 2010) (updated as DESeq2 (Love, Huber et al. 2014)), edgeR (Robinson, McCarthy et al. 2010, Zhou, Lindsay et al. 2014), NOISeq (Tarazona, García-Alcalde et al. 2011), PoissonSeq (Li, Witten et al. 2011), and SAMseq (samr) (Li and Tibshirani 2013) have been developed. However, the majority of biologists who lack of programming skills are not able to make full use of these tools since these tools provide little interaction and visualization functions that can help users run the analysis and interpret results intuitively. Moreover, the results from different analysis tools could be inconsistent. Therefore, an interactive tool that implements and combines these differential expression analysis tools is particularly helpful to those researchers with little bioinformatics knowledge.
Here, we developed a web server called "Interactive Differential Expression Analyzer (IDEA)" for differential gene expression analysis of count data using R (R Core Team 2014), Shiny (RStudio Inc. 2014) and JavaScript. With the help of this web server, users can quickly and easily access the most often used differential expression analysis tools. IDEA is highly interactive and will provide good visualization. Additionally, a Score based on robust rank aggregation (RRA) (Kolde, Laur et al. 2012) integrates the result rank lists from different tools to refine the set of differentially expressed features.
[Click here to redirect to IDEA website.](http://idea.biocuckoo.org)Screen shoot of IDEA
Web server is very easy to access and can finish analysis while small dataset(less than 5M) were submitted. However, Limited to remote server resouces, the web page usually stucked when multible user operated or with bigger dataset. To solve this, We thus released an R package that packed the whole application for users to run analysis in R environment locally .
Before install the IDEA package, please read this markdown file carefully;
First, to run IDEA functionally in local machine, you must make sure that all the dependencies were well installed.（We recommanded users using Rstudio as their console to make installation procedure more easily)
To check the dependencies, one can simply type
library("Packages for check")To date, the current version(IDEA 1.0) works 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()
```R
devtools::install_github( "ebailey78/shinyBS")
We also list the command to install the related packages:
cDep <- c("abind")
#dependencies from BIOCONDUCTOR
bcDep <- c("Biobase", "BiocGenerics", "S4Vectors", "IRanges", "GenomeInfoDb", "GenomicRanges")
#target from CRAN
cTgt <- c("PoissonSeq","FactoMineR","samr","ggplot2","VennDiagram","RobustRankAggreg","shiny","rmarkdown")
#target from BIOCONDUCTOR
bcTgt <- c("edgeR", "DESeq2")
###INSTALLED PACKAGES
#get installed list
inst <- packageStatus()$inst
#check and install DEPENDENCIES from CRAN
for(i in 1:length(cDep)){
tag = which(inst$Package == cDep[i])
if(length(tag)){
remove.packages(cDep[i])
}
install.packages(cDep[i])
}
#check and install DEPENDENCIES from BIOCONDUCTOR
source("http://bioconductor.org/biocLite.R")
for(i in 1:length(bcDep)){
tag = which(inst$Package == bcDep[i])
if(length(tag))
remove.packages(bcDep[i])
biocLite(bcDep[i])
}
#check and install TARGET packages
for(i in 1:length(cTgt)){
install.packages(cTgt[i])
}
for(i in 1:length(bcTgt)){
biocLite(bcTgt[i])
}
devtools::install_github("shiny-incubator", "rstudio")
devtools::install_github( "ebailey78/shinyBS")Second, to install the latest development build 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")The above command can automaticly install the several dependencies which allows users skipping some installation steps; However, the shinyBS package would be latest version which will result in incompatible with IDEA. User can remove it and reinstall the right version to avoid this; Alternately, if you have installed dependencies manually, you can then install IDEA pakcage alone with following command :
if (!require("devtools"))
install.packages("devtools")
devtools::install_github("likelet/IDEA",dependencies = FALSE)or download it from git then install package with install command
install.packages("path_to_IDEA.tar.gz/.zip", repos = NULL, type="source")For computer with GUI
Clone repository into local path and run as a Shiny App
example:
Clone repository into local directory '/Document/IDEA' (so that ui.R locates as '/Document/IDEA/ui.R')
then run in R under work directory of '/Document' :
runApp("IDEA")Also, after install IDEA pakcages with no error print, users can simply input
```R runIDEA() ``` function to run application locally; Since there is only one function in this package, you can also print help massege in your R console;
For server or computer without GUI(Run IDEA on a sever)
Install shiny-server first and finish the configurations step refers to http://rstudio.github.io/shiny-server/latest/
Clone this package and install the dependencies mentioned above in your R environment;
Copy IDEA folder under inst dir into /srv/shiny-sever/ (or orther app location you configured in shiny-sever)
Configure the server network/firewall options like open the shiny port(3838 default), internal IP access (please refer to shiny-server configuration step);
Input the server ip address with port number and enjoy your IDEA analysis trip :).
R version 3.1.2
Packages:
Shiny (0.12.2), ShinySky(0.1.2), shinyIncubator (3.2.4),shinyBS(0.25) and their dependencies
DESeq2 (1.6.2), edgeR (3.2.4), SAMseq (2.0), PoissonSeq (1.1.2), NOISeq (2.8.0) and their dependencies
ggplot2, reshape, plyr, scale, RColorBrewer and other packages needed in plotting
Documentation
First stable version released. To view user guide, please visit http://idea.biocuckoo.org and refers to HELP section Developer Information
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. Several packages can not be installed with errors returned, how to fix this?
***2. "Error : unrecognized fields specified in html_dependency: attachment" while clicks the download report button***:
***3. "Error: pandoc version 1.12.3 or higher is required and was not found." while clicks the download report button***:
Jian Ren, [email protected]
Qi Zhao, [email protected]
Qi Zhao, [email protected]
Peng Nie, [email protected]
Rucheng Diao, [email protected]
Lichen Sun, [email protected]
Yi Shi, [email protected]
Qi Zhao, Peng Nie
Please feel free contact us.
Copyright © 2015. The CUCKOO Workgroup. All Rights Reserved
For more useful tools/applications, please go to biocuckoo.org
If you using any one of IDEA intergrated R packages in your publications, please cite the related packages bycitations(packagesname);
Also, if you adopted intergrated analysis module, report page as well as other fancy plots generated by IDEA, please cite the IDEA in the same way;
The pulication of IDEA is in the preparation, we will release the citation info as soon as possible.