This R package contains the R-Shiny application v1.5.2 developed to perform differential gene expression analysis.
- dgeAnalysis manual: https://github.com/LUMC/dgeAnalysis/blob/master/MANUAL.pdf
- Install the "devtools" package (if not already installed):
install.packages("devtools")
- Install the "dgeAnalysis" package:
library("devtools")
devtools::install_github("LUMC/dgeAnalysis")
- Launch the application:
library("dgeAnalysis")
dgeAnalysis::startApp()
- Start the application
- Go to "Data upload"
- Upload files: (both CSV and TSV is accepted)
- Samplesheet (metadata), Contains information about each sample.
- Count data, Contains the read alignment results (read counts per feature).
- Annotation, Contains more information about genes (location, length, etc.).
- Set a comparison
- Run the analysis
- View the results
Note: In the folder "exampleData" there is a .zip file, containing three data files. These example files can be used to e.g. check if the application is working and/or your data has the correct format.
R version: 4.1+
Linux install libraries:
sudo apt-get update && apt-get install \
build-essential \
gdebi-core \
pandoc \
pandoc-citeproc \
libcairo2-dev \
libjpeg-dev \
libxt-dev \
libssl-dev \
libcurl4-gnutls-dev \
libxml2-dev \
libcurl4-openssl-dev \
-y
Windows install RTools and pandoc:
R 4.0 and up:
https://cran.r-project.org/bin/windows/Rtools
Pandoc:
https://pandoc.org/installing.html
If there are problems installing the application, it might be worth to try installing specific packages manually:
## Shiny environment
if (!require("shiny")) install.packages("shiny")
if (!require("shinydashboard")) install.packages("shinydashboard")
if (!require("shinyWidgets")) install.packages("shinyWidgets")
if (!require("shinycssloaders")) install.packages("shinycssloaders")
if (!require("shinyjs")) install.packages("shinyjs")
## Differential expression analysis
if (!require("BiocManager")) install.packages("BiocManager")
if (!require("knitr")) install.packages("knitr")
if (!require("SummarizedExperiment")) BiocManager::install("SummarizedExperiment")
if (!require("edgeR")) BiocManager::install("edgeR")
if (!require("limma")) BiocManager::install("limma")
if (!require("DESeq2")) BiocManager::install("DESeq2")
if (!require("tidyr")) install.packages("tidyr")
if (!require("scales")) install.packages("scales")
if (!require("broom")) install.packages("broom")
if (!require("plotly")) install.packages("plotly")
if (!require("Rtsne")) install.packages("Rtsne")
if (!require("rmarkdown")) install.packages("rmarkdown")
## Enrichment analysis
if (!require("gprofiler2")) install.packages("gprofiler2")
if (!require("igraph")) install.packages("igraph")