scMerge

DOI: 10.18129/B9.bioc.scMerge    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see scMerge.

scMerge: Merging multiple batches of scRNA-seq data

Bioconductor version: 3.9

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

Maintainer: Kevin Wang <kevin.wang at sydney.edu.au>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-3
Depends	R (>= 3.6.0)
Imports	BiocParallel, cluster, distr, doSNOW, foreach, igraph, irlba, iterators, matrixStats, M3Drop(>= 1.9.4), parallel, pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>= 0.3.3.4.0), ruv, rsvd, S4Vectors, SingleCellExperiment, SummarizedExperiment
LinkingTo	Rcpp (>= 0.12.18), RcppEigen, testthat
Suggests	BiocStyle, covr, knitr, Matrix, rmarkdown, scales, scater, testthat
SystemRequirements
Enhances
URL	https://github.com/SydneyBioX/scMerge
BugReports	https://github.com/SydneyBioX/scMerge/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scMerge_1.0.0.tar.gz
Windows Binary	scMerge_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	scMerge_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scMerge
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scMerge
Package Short Url	https://bioconductor.org/packages/scMerge/
Package Downloads Report	Download Stats