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massonix / SLOcatoR

SLOcatoR is an R package to annotate single-cell transcriptomes and open chromatin profiles from secondary lymphoid organs using the tonsil atlas as reference
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SLOcatoR

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

Installation

You can install the development version of SLOcatoR from GitHub with:

# install.packages("devtools")
devtools::install_github("massonix/SLOcatoR")

Contact

If you have any doubts or suggestions feel free to contact us by email or on twitter.