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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| scMerge | HTML | R Script |
| scMerge2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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 | BatChef, 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_1.29.0.tar.gz |
| Windows Binary (x86_64) | scMerge_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | scMerge_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | scMerge_1.29.0.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 |