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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 (3.19)

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 sydney.edu.au>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scMerge")

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

Documentation

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

browseVignettes("scMerge")
scMerge HTML R Script
scMerge2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.19.0
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
System Requirements
URL https://github.com/SydneyBioX/scMerge
Bug Reports https://github.com/SydneyBioX/scMerge/issues
See More
Suggests BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger
Linking To
Enhances
Depends On Me
Imports Me singleCellTK
Suggests Me Cepo
Links To Me
Build Report Build Report

Package Archives

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

Source Package scMerge_1.19.0.tar.gz
Windows Binary scMerge_1.19.0.zip (64-bit only)
macOS Binary (x86_64) scMerge_1.19.0.tgz
macOS Binary (arm64) scMerge_1.19.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scMerge
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scMerge
Bioc Package Browser https://code.bioconductor.org/browse/scMerge/
Package Short Url https://bioconductor.org/packages/scMerge/
Package Downloads Report Download Stats