scMerge

DOI: 10.18129/B9.bioc.scMerge  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scMerge.

scMerge: Merging multiple batches of scRNA-seq data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	scMerge
HTML	R Script	scMerge2
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.16.0
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 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
LinkingTo
Suggests	BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger
SystemRequirements
Enhances
URL	https://github.com/SydneyBioX/scMerge
BugReports	https://github.com/SydneyBioX/scMerge/issues
Depends On Me
Imports Me	singleCellTK
Suggests Me	Cepo
Links To Me
Build Report

Package Archives

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

Source Package	scMerge_1.16.0.tar.gz
Windows Binary	scMerge_1.16.0.zip
macOS Binary (x86_64)	scMerge_1.16.0.tgz
macOS Binary (arm64)	scMerge_1.16.0.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