scMerge is a R package for merging and normalising single-cell RNA-Seq datasets.
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("ruv", "rsvd", "igraph", "pdist", "proxy", "foreach", "doSNOW", "distr")) devtools::install_github("theislab/kBET") # Some BioConductor packages required by scMerge # try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite(c("SingleCellExperiment", "M3Drop")) # Installing scMerge and the data files using devtools::install_github("SydneyBioX/scMerge.data") devtools::install_github("SydneyBioX/scMerge")
You can find the vignette at our website: https://sydneybiox.github.io/scMerge/index.html.
You can find a list of case studies here: https://sydneybiox.github.io/scMerge/articles/.
If you have any enquires, especially about performing
scMerge integration on your data, then please contact [email protected]
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
BioRxiv preprint: https://www.biorxiv.org/content/early/2018/08/16/393280
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