A Shinydashboard for visualizing RNAseq data analyzed with DESeq2. For demonstration purposes, the script downloads the countmatrix and phenodata from Mov10 bulk RNAseq data made available at the Harvard Chan Bioinformatic Core (https://github.com/hbctraining/DGE_workshop). This app uses some of the analytical tools employed by the workshop. Thus, for further details on explanation of the DESeq2 analysis, please refer to the HBC workshop link. The material and presentation of workshop was very insightful. The shinydashboard codes were synthesized from the many talented answers to questions on stackoverflow and the shinydashboard help website.
Any questions or feedback are welcome. Feel free to modify and repurpose the app. Although it is not optimized and needs some work to make figures more clearer (ex. font size), it is a work in progress. There are many other well developed analytical and visualization tools available, but this provides a starting point for your own implementation in a shinydashboard.
This app was developed in a docker container of a modified rocker/rstudio (R-version:3.6.1 and RStudio-version:1.2.1335) image described here and here running on a Ubuntu 18.04LTS. Perhaps at another point I will put up a dockerfile for the image/container with a full working version so as to minimize the installations of libraries and packages required. Also it is very possible to make this into a portable app using Electron, Shiny, and R; see here, here, and here.
Here are the libraries required for the app. So ensure that they are installed. Some are directly from CRAN and others are to be installed via BiocManager from Bioconductor.
example:
install.packages("shiny")
example:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
library(shiny)
library(shinydashboard)
library(shinyjs) # for dynamically displaying tab titles
library(DESeq2)
library(pheatmap)
library(RColorBrewer)
library(ggplot2)
library("ggrepel") #Avoid overlapping labels
library(scales)
library(DT)
library(tidyr)
OTHER ATTACHED PACKAGES
jsonlite_1.6 Matrix_1.2-17 viridisLite_0.3.0 DT_0.9
shiny_1.4.0 shinyjs_1.0 shinydashboard_0.7.1
ggfortify_0.4.7 data.table_1.12.4 tidyr_1.0.0
ggrepel_0.8.1 dplyr_0.8.3 magrittr_1.5
DESeq2_1.24.0 pheatmap_1.0.12 S4Vectors_0.22.1
DelayedArray_0.10.0 BiocParallel_1.18.1 SummarizedExperiment_1.14.1
matrixStats_0.55.0 Biobase_2.44.0 BiocGenerics_0.30.0
GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.3
RColorBrewer_1.1-2 ggplot2_3.2.1 scales_1.0.0
Below are screenshots of working app
https://github.com/mppl1/shinydashboard-DESeq2/blob/master/Waldtest.png
