shinyCircos-V2.0 is the updated version of shinyCircos. In shinyCircos-V2.0, we developed several advanced features, designed brand-new user interface, and fixed bugs detected in shinyCircos.
Welcome to the telegram group https://t.me/+NadFeZazBBc2Y2U1.
shinyCircos-V2.0 is deployed at https://venyao.xyz/shinyCircos/, and https://asiawang.shinyapps.io/shinyCircos/ for online use.
User can choose to run shinyCircos-V2.0 installed locally for a more preferable experience.
Step 1: Install R and RStudio
Before running the app you will need to have R and RStudio installed (tested with R 3.3.3 and RStudio 1.0.143).
Please check CRAN (https://cran.r-project.org/) for the installation of R.
Please check https://www.rstudio.com/ for the installation of RStudio.
Step 2: Install the R Shiny package and other packages required by shinyCircos-V2.0
Start an R session using RStudio and run these lines:
install.packages("shiny")
install.packages("circlize")
install.packages("bs4Dash")
install.packages("DT")
install.packages("RColorBrewer")
install.packages("shinyWidgets")
install.packages("data.table")
install.packages("shinyBS")
install.packages("sortable")
install.packages("shinyjqui")
install.packages("shinycssloaders")
install.packages("colourpicker")
install.packages("gridBase")
install.packages("randomcoloR")
install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")
Step 3: Start the app
Start an R session using RStudio and run these lines:
shiny::runGitHub("shinyCircos-V2.0", "YaoLab-Bioinfo")
This command will download the code of shinyCircos from GitHub to a temporary directory of your computer and then launch the shinyCircos app in the web browser. Once the web browser was closed, the downloaded code of shinyCircos would be deleted from your computer. Next time when you run this command in RStudio, it will download the source code of shinyCircos from GitHub to a temporary directory again. This process is frustrating since it takes some time to download the code of shinyCircos from GitHub.
Users are suggested to download the source code of shinyCircos from GitHub to a fixed directory of your computer, such as 'E:\apps' on Windows. A zip file named "shinyCircos-V2.0-master.zip" will be downloaded to your computer. Move this file to "E:\apps" and unzip this file. Then a directory named "shinyCircos-V2.0-master" will be generated in "E:\apps". The scripts "server.R" and "ui.R" can be found in "E:\apps\shinyCircos-V2.0-master".
Then you can start the shinyCircos app by running these lines in RStudio.
library(shiny)
runApp("E:/apps/shinyCircos-V2.0-master", launch.browser = TRUE)