R Shiny app for comparison of annotations such as (i) cell type assignments (e.g., from different mapping/clustering algorithms), (ii) donor metadata (e.g., donor, sex, age), and (iii) cell metadata (e.g., anatomic location, QC metrics).
(You only need do this step once).
- Install R
- Install RStudio
- Install the following packages in R Studio:
packages <- setdiff(c("remotes","dplyr","data.table","DT","feather","ggplot2","ggbeeswarm","rbokeh","shiny","UpSetR","anndata"), installed.packages()[,"Package"])
if(length(packages)>0) install.packages(packages)
remotes::install_github("AllenInstitute/scrattch.io")
- Download the files from this repo (you may want to repeat this step occasionally to check for updates!)
- In RStudio, open the file
ui.R
and click the "Run App" button in the upper right corner of the screen - Enter the location of your annotation file in the "Location of annotation information" box (it should be pointing to some example data by default)
- Explore!
Please share any comments, suggestions, bugs, or any other thoughts using the button in the app.