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


scMerge is available on Bioconductor (https://bioconductor.org/packages/scMerge). You can install it using:

## Install scMerge from Bioconductor, requires R 3.6.0 or above
## You can also try to install the Bioconductor devel version of scMerge:
BiocManager::install("scMerge", version = "devel")


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/.

Stably Expressed Genes

Stably expressed genes identified from this study can be extracted by

segList$human$human_scSEG # human SEG
segList$mouse$mouse_scSEG # mouse SEG

Or download csv files here (human SEG: link; mouse SEG: link)

For more detailed information and evaluation about SEG, please see our publication https://doi.org/10.1093/gigascience/giz106.

Contact us

If you have any enquiries, especially about performing scMerge integration on your own data, then please contact . You can also open an issue on GitHub.


scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

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

Our manuscript published at PNAS can be found here.