Dataset Collections

The Cell Browser allows you to group related datasets into single-level collections. Collections will displayed in your cell browser alongside all of your other datasets; when you open a collection, it will show you all of the datasets within it.

First, to enable the collections feature, you must add a single line pointing to the directory where all of your single-cell data lives to your ~/.cellbrowser.conf:

collDir='/celldata/'

Next, for each dataset you would like to be a part of a collection, add a collections line to the dataset’s cellbrowser.conf, such as:

collections = ["organoids"]

This will create a single collection in your cell browser named organoids. You can specify multiple collection names separated by a comma (e.g. ["organoids", "human"]).

Then, describe the menu entry for the collection by placing a cellbrowser.conf for it somewhere within your collDir. This minimal cellbrowser.conf file only needs to contains the name, shortLabel and tags settings:

mkdir -p /celldata/organoids
cd /celldata/organoids
echo 'name="organoids"' > cellbrowser.conf
echo 'shortLabel="Brain Organoids"' >> cellbrowser.conf
echo 'tags=["10x"]' >> cellbrowser.conf

Now you can describe your collection as discussed under the Describing datasets section. Put the desc.conf file into the same directory as the cellbrowser.conf you just created.

Now run cbBuild for each of the datasets that you would like to be in the collection. If you view your cell browser on the web, you should see this new collection present. Additionally, when viewing a dataset in a collection, you can move quickly between it and other datasets in the same collection using the “Collection” dropdown menu.