DOI: 10.18129/B9.bioc.scMerge    

This is the development version of scMerge; for the stable release version, see scMerge.

scMerge: Merging multiple batches of scRNA-seq data

Bioconductor version: Development (3.14)

Like all gene expression data, single-cell RNA-seq (scRNA-Seq) data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple scRNA-Seq data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of scRNA-Seq data.

Author: Yingxin Lin [aut, cre], Kevin Wang [aut], Sydney Bioinformatics and Biometrics Group [fnd]

Maintainer: Yingxin Lin <yingxin.lin at>

Citation (from within R, enter citation("scMerge")):


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script scMerge
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.9.0
In Bioconductor since BioC 3.9 (R-3.6) (2.5 years)
License GPL-3
Depends R (>= 3.6.0)
Imports BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop(>= 1.9.4), parallel, pdist, proxy, ruv, S4Vectors(>= 0.23.19), SingleCellExperiment(>= 1.7.3), SummarizedExperiment
Suggests BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, scater, testthat, badger
Depends On Me
Imports Me singleCellTK
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scMerge_1.9.0.tar.gz
Windows Binary (32- & 64-bit)
macOS 10.13 (High Sierra) scMerge_1.9.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: