WB-DEGS require the pre-installation of one of the recent versions of R, a free software environment for statistical computing and graphics. R can be downloaded from http://cran.r-project.org/.
After installing R, please refer to installScript.R file, which is located under the WB-DEGS directory, and execute it to download and install all necessary packages.
from Cran:
install.packages("shiny")
install.packages("VennDiagram")
from Bioconductor:
source("http://bioconductor.org/biocLite.R")
biocLite("affy")
biocLite("affyPLM")
biocLite("limma")
biocLite("siggenes")
biocLite("twilight")
biocLite("genefilter")
The table below gives a quik description about the packages required by this application.
| Package | Description |
|---|---|
| shiny | Web Application Framework for R, Shiny makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort. |
| VennDiagram | A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. |
| affy | The package contains functions for exploratory oligonucleotide array analysis. |
| affyPLM | A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. |
| limma | LIMMA is a library for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. |
| siggenes | Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Analyses of Microarrays (EBAM). |
| twilight | Package 'twilight' : Estimation of local false discovery rate. |
| genefilter | Methods for filtering genes from microarray experiments, contains Some basic functions for filtering genes. |