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 (3.15)

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: Yingxin Lin <yingxin.lin at sydney.edu.au>, Kevin Wang <kevin.wang at sydney.edu.au>, Sydney Bioinformatics and Biometrics Group Lin <bioinformatics at maths.usyd.edu.au>

Maintainer: Yingxin Lin <yingxin.lin at sydney.edu.au>

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

Installation

To install this package, start R (version "4.2") 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

PDF   Reference Manual

Details

biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.11.0
In Bioconductor since BioC 3.9 (R-3.6) (2.5 years)
License GPL-3
Depends R (>= 3.6.0)
Imports BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop(>= 1.9.4), parallel, pdist, proxy, ruv, S4Vectors(>= 0.23.19), SingleCellExperiment(>= 1.7.3), SummarizedExperiment
LinkingTo
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 singleCellTK
Suggests Me Cepo
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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/
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