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scMerge: Merging multiple batches of scRNA-seq data

Bioconductor version: Release (3.19)

Like all gene expression data, single-cell 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 single-cell data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of single-cell 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 "4.4") and enter:

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


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:

scMerge HTML R Script
scMerge2 HTML R Script
Reference Manual PDF


biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-3
Depends R (>= 3.6.0)
Imports BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop(>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors(>= 0.23.19), SingleCellExperiment(>= 1.7.3), SummarizedExperiment
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Suggests BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger
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Depends On Me
Imports Me singleCellTK
Suggests Me Cepo
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Follow Installation instructions to use this package in your R session.

Source Package scMerge_1.20.0.tar.gz
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macOS Binary (x86_64) scMerge_1.20.0.tgz
macOS Binary (arm64) scMerge_1.20.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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