scMerge

DOI: 10.18129/B9.bioc.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 (3.11)

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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script scMerge
PDF   Reference Manual
Text   NEWS

Details

biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.3.0
In Bioconductor since BioC 3.9 (R-3.6) (0.5 years)
License GPL-3
Depends R (>= 3.6.0)
Imports BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop(>= 1.9.4), parallel, pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>= 0.3.3.4.0), ruv, S4Vectors(>= 0.23.19), SingleCellExperiment(>= 1.7.3), SummarizedExperiment
LinkingTo Rcpp (>= 0.12.18), RcppEigen, testthat
Suggests BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, scater, testthat, badger
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_1.3.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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

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