An R package for performing cell typing in SMI and other single cell data
Manuscript: https://www.biorxiv.org/content/10.1101/2022.10.19.512902v1.abstract
Citing Insitutype: Danaher P, Zhao E, Yang Z, Ross D, Gregory M, Reitz Z, Kim TK, Baxter S, Jackson S, He S, Henderson DA. Insitutype: likelihood-based cell typing for single cell spatial transcriptomics. bioRxiv. 2022 Jan 1.
- R (>= 3.5.0)
- UNIX, Mac or Windows
- Rcpp library (>= 1.0.9)
- see DESCRIPTION for full dependencies
See the "vignettes" folder. Vignettes should run in <5 minutes.
Run "insitutype" for unsupervised or semi-supervised clustering. Run "insitutypeML" for supervised cell typing. See the vignettes for example workflows.
The full results of the Insitutype manuscript can be reproduced with the code in this repo: https://github.com/Nanostring-Biostats/InSituType-manuscript-analyses
devtools::install_github("https://github.com/Nanostring-Biostats/InSituType")
Installation should take < 2 mins on a normal desktop computer.
