In this repository, you will find code and R objects to support the R/Shiny app for exploring rbm8a knockout RNA-seq experiments interactively.
Please see the corresponding preprint:
Kocere, A.; Chiavacci, E.; Mendez-Acevedo, K. M.; Soneson, C.; Hiltabidle, M. S.; Raghunath, A.; Macgowan, J. S.; Shavit, J. A.; Panakova, D.; Williams, M. L. K.; Robinson, M. D.; Mosimann, C.; Burger, A.: TAR Syndrome-associated Rbm8a deficiency causes hematopoietic defects and attenuates Wnt/PCP signaling. bioRxiv doi: https://doi.org/10.1101/2023.04.12.536513. Posted April 20, 2023.
Instructions follow below for viewing the dataset locally via R.
If R is not already installed, find your closest mirror here and follow the instructions for installation; if using RStudio, you can download it from here)
Download the repository, either from the command line with a command like:
git clone https://github.com/markrobinsonuzh/rbm8a-rnaseq-explorer.git
or, download a snapshot of the repository using the green Code button above (e.g., click on Download ZIP and then unzip the files of the repository in a reasonable location locally).
Then, start an R session and set the current working directory to where rbm8a-rnaseq-explorer was placed. (TIP: if using RStudio, you can double-click on the rbm8a-rnaseq-explorer.Rproj file and an R session will be started with the directory correctly set.)
If not already installed, you will need to install the following packages (cut-and-paste into the console):
install.packages("BiocManager", quiet = TRUE)
pkgs <- c("shiny","ggplot2","ggrepel",
"GGally", "dplyr", "tidyr",
"Gviz", "ComplexHeatmap", "reshape2",
"circlize", "gridExtra", "rtracklayer")
BiocManager::install(pkgs)
To run the app, run:
source("app.R")
Note that for the coverage tracks to be displayed, you will need to download 7 BW (bigwig) files from here and place them in the starbigwig directory.
See about_app.md.