scMerge
scMerge: Merging multiple batches of scRNA-seq data
Bioconductor version: Release (3.20)
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>
citation("scMerge")):
Installation
To install this package, start R (version "4.4") 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")| scMerge | HTML | R Script |
| scMerge2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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 |
| System Requirements | |
| URL | https://github.com/SydneyBioX/scMerge |
| Bug Reports | https://github.com/SydneyBioX/scMerge/issues |
See More
| Suggests | BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | singleCellTK |
| Suggests Me | Cepo |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scMerge_1.22.0.tar.gz |
| Windows Binary (x86_64) | scMerge_1.22.0.zip (64-bit only) |
| macOS Binary (x86_64) | scMerge_1.22.0.tgz |
| macOS Binary (arm64) | scMerge_1.22.0.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 |