Smmit performs integration both across samples and modalities to produce a single UMAP space. It first uses harmony to integrate across samples and then uses Seurat weighted nearest neighbor function to integrate across modalities.
Smmit software can be installed via Github.
Users should have R installed on their computer before installing Smmit. R can be downloaded here: http://www.r-project.org/.
To install the latest version of Smmit package via Github, run following commands in R:
if (!require("devtools"))
install.packages("devtools")
devtools::install_github("zji90/Smmit")
Please visit this webpage for the user manual: https://github.com/zji90/Smmit/blob/master/vignettes/Smmit.pdf
Author: Changxin Wan, Zhicheng Ji
Report bugs and provide suggestions by sending email to:
Maintainer: Zhicheng Ji (zhicheng.ji@duke.edu)
Or open a new issue on this Github page