scMerge
This is the development version of scMerge; for the stable release version, see scMerge.
All Bioconductor versions of scMerge
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9
scMerge: Merging multiple batches of scRNA-seq data
Bioconductor version: 3.24 · Package version: 1.29.0
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 sydney.edu.au>
Citation
From within R, enter citation("scMerge"):
Yingxin Lin, Kevin Wang. scMerge: scMerge: Merging multiple batches of scRNA-seq data. doi:10.18129/B9.bioc.scMerge, R package version 1.29.0, https://bioconductor.org/packages/scMerge.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scMerge")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.29.0 |
| License | GPL-3 |
| URL | https://github.com/SydneyBioX/scMerge |
| Bug Reports | https://github.com/SydneyBioX/scMerge/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7 years) |
| Downloads rank | 414 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/scMerge/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | scMerge_1.29.0.tar.gz |
| Windows binary (x86_64) | scMerge_1.29.0.zip |
| macOS binary (arm64) | scMerge_1.29.0.tgz |
| macOS binary (x86_64) | scMerge_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scMerge |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scMerge |
| Package Downloads Report | Download Stats |
Dependencies
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
Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger