Update: given that the tonsil atlas reference has been included in Azimuth, we refer users to that application to annotate their single-cell transcriptomes using our reference. For a finer-grained annotation, we recommend users downloading their dataset of interest (e.g. CD4 T cells) using our HCATonsilData package. The current form of SLOcatoR serves to provide a transparent package to show how we annotated our cells from the validation cohort and connected the different data modalities. This is exemplified with the mapping and annotation of CD4 T cells from the validation cohort onto the discovery cohort
You can install the development version of SLOcatoR from GitHub with:
# install.packages("devtools")
devtools::install_github("massonix/SLOcatoR")If you have any doubts or suggestions feel free to contact us by email or on twitter.