This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scMerge.
Bioconductor version: 3.16
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 [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")
):
To install this package, start R (version "4.2") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scMerge")
HTML | R Script | scMerge |
Reference Manual | ||
Text | NEWS |
biocViews | BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
Version | 1.14.0 |
In Bioconductor since | BioC 3.9 (R-3.6) (4 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 |
Follow Installation instructions to use this package in your R session.
Source Package | scMerge_1.14.0.tar.gz |
Windows Binary | scMerge_1.14.0.zip (64-bit only) |
macOS Binary (x86_64) | scMerge_1.14.0.tgz |
macOS Binary (arm64) | scMerge_1.14.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/scMerge |
Source Repository (Developer Access) | git clone [email protected]:packages/scMerge |
Bioc Package Browser | https://code.bioconductor.org/browse/scMerge/ |
Package Short Url | https://bioconductor.org/packages/scMerge/ |
Package Downloads Report | Download Stats |
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