InSituType

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.

System requirements

R (>= 3.5.0)
UNIX, Mac or Windows
Rcpp library (>= 1.0.9)
see DESCRIPTION for full dependencies

Demo

See the "vignettes" folder. Vignettes should run in <5 minutes.

Instructions for use

Run "insitutype" for unsupervised or semi-supervised clustering. Run "insitutypeML" for supervised cell typing. See the vignettes for example workflows.

FAQs and tips:

https://github.com/Nanostring-Biostats/InSituType/FAQs.md

Reproduction instructions

The full results of the Insitutype manuscript can be reproduced with the code in this repo: https://github.com/Nanostring-Biostats/InSituType-manuscript-analyses

Installation

# Make sure Matrix and irlba are both up to date (otherwise versioning issues cause prcomp_irlba to error out):
# (This is required as of Feb 2024; with any luck these packages will fix their versioning issues soon and this will not be necessary.)
install.packages("Matrix", type = "source")
install.packages("irlba", type = "source")

# Install Insitutype:
devtools::install_github("https://github.com/Nanostring-Biostats/InSituType")

Installation should take < 2 mins on a normal desktop computer.

Nanostring-Biostats / InSituType

readme