AllenInstitute / ACE

R Shiny app for comparison of annotations (e.g., cell type assignments)

annotation_comparison

(NOTE: This branch is currently out of date. Use the dev branch for now. I'll merge them soon).

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).

How to use

Setup RStudio

(You only need do this step once).

1. Install R
2. Install RStudio
3. 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")

4. Download the files from this repo (you may want to repeat this step occasionally to check for updates!)

Run the app

1. In RStudio, open the file ui.R and click the "Run App" button in the upper right corner of the screen
2. Enter the location of your annotation file in the "Location of annotation information" box (it should be pointing to some example data by default)
3. Explore!

Reporting issues or suggestions

Please share any comments, suggestions, bugs, or any other thoughts using the button in the app.