Skip to content

A shiny application to perform differential gene expression analysis of count data using DESeq2. The app also allows unsupervised exploration of data using PCA and hierarchical clustering.

License

Notifications You must be signed in to change notification settings

bixBeta/DESeq2-shiny

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

60 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

R-CMD-check

PCA-Explorer + DGE analysis using DESeq2-Shiny

The limited version of this app can be accessed here: https://bixbeta.shinyapps.io/PCA-Explorer/

To run locally (strongly recommended), use the following instructions:

git clone this repository using git clone https://github.com/bixBeta/DESeq2-shiny.git
or using the green (Code/Clone) button on top of this page.
cd to DESeq2-shiny/PCA-Explorer
copy the path for the ui and server files by using pwd, we will need this path later.

Launch R Console on a Mac or PC and INSTALL the following packages:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
if (!requireNamespace("DESeq2", quietly = TRUE)) BiocManager::install("DESeq2")
if (!requireNamespace("dplyr", quietly = TRUE)) install.packages("dplyr")
if (!requireNamespace("plotly", quietly = TRUE)) install.packages("plotly")
if (!requireNamespace("shiny", quietly = TRUE)) BiocManager::install("shiny")
if (!requireNamespace("tibble", quietly = TRUE)) install.packages("tibble")
if (!requireNamespace("DT", quietly = TRUE)) install.packages("DT")
if (!requireNamespace("shinyjs", quietly = TRUE)) BiocManager::install("shinyjs")

Once all packages are installed:

From R Console type shiny::runApp('~/path/to/DESeq2-shiny/PCA-Explorer')# (paste the copied path here)
Alternatively, from a bash terminal type R -e shiny::runApp('~/path/to/DESeq2-shiny/PCA-Explorer')
Copy the ip address and paste it in a web browser to launch the app

countMatrix and target file

Example CountMatrix and metadata target files are available in the PCA-Explorer/example folder.

In the target file, label and group columns are mandatory.

In the label column, please refrain from using any special characters, only . is acceptable e.g. Sample.1

The label column fields must match the column names of the countMatrix.txt file.
e.g. Sample.1 label must have a corresponding Sample.1 counts column in the countMatrix.txt file

All labels are case-sensitive.

Demo

alt text

About

A shiny application to perform differential gene expression analysis of count data using DESeq2. The app also allows unsupervised exploration of data using PCA and hierarchical clustering.

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published