README.md

scMerge

scMerge is a R package for merging and normalising single-cell RNA-Seq datasets.

Installation

The installation process could take up to 5 minutes, depending if you have some of the packages pre-installed.

# Some CRAN packages required by scMerge
install.packages(c("BiocManager", "distr", "doSNOW", "foreach", "igraph", "irlba", "iterators", "pdist", "proxy",  "Rcpp", "RcppEigen", "rsvd", "ruv"))

# Some BioConductor packages required by scMerge
BiocManager::install(c("BiocParallel", "M3Drop", "SingleCellExperiment"))

# Some GitHub packages required by scMerge
devtools::install_github("theislab/kBET")
devtools::install_github("SydneyBioX/scMerge.data")
devtools::install_github("SydneyBioX/scMerge")

Vignette

You can find the vignette at our website: https://sydneybiox.github.io/scMerge/index.html.

Case studies

You can find a list of case studies here: https://sydneybiox.github.io/scMerge/articles/.

Contact us

If you have any enquires, especially about performing scMerge integration on your data, then please contact [email protected]

Reference

scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication

Yingxin Lin, Shila Ghazanfar, Kevin Y.X. Wang, Johann A. Gagnon-Bartsch, Kitty K. Lo, Xianbin Su, Ze-Guang Han, John T. Ormerod, Terence P. Speed, Pengyi Yang, Jean Y. H. Yang

doi: https://doi.org/10.1101/393280

BioRxiv preprint: https://www.biorxiv.org/content/early/2018/08/16/393280



SydneyBioX/scMerge documentation built on Jan. 21, 2019, 6:59 a.m.