annotation_comparison

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). This tool is now hosted on shinyapps.io.

Additionally, this tool can compare results across more than two taxonomies as once. The two primary use cases are (1) annotating a novel taxonomy with information from multiple existing taxonomies and (2) comparison of data from multiple studies of Alzheimer's disease (like in the example below).

How to use

Either visit the tool hosted on shinyapps.io or follow the instructions below to run locally in R Studio. Currently, you need to run it locally to point to external files stored locally, but for most use cases, the hosted version is recommended.

Setup RStudio

(You only need do this step once).

1. Install R
2. Install RStudio
3. Install the following packages in R Studio:

   options(install.packages.compile.from.source = "always")
   packages <- setdiff(c("remotes","dplyr","data.table","DT","feather","ggplot2","ggbeeswarm","shiny","UpSetR","anndata"), installed.packages()[,"Package"])
   if(length(packages)>0) install.packages(packages, type = "both")
   remotes::install_github("AllenInstitute/scrattch.io")
   remotes::install_github("bokeh/rbokeh")

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, or by submitting an issue.