DOI: 10.18129/B9.bioc.scMerge    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scMerge.

scMerge: Merging multiple batches of scRNA-seq data

Bioconductor version: 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 < at>

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biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.4.0
In Bioconductor since BioC 3.9 (R-3.6) (1.5 years)
License GPL-3
Depends R (>= 3.6.0)
Imports BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, dplyr, igraph, M3Drop(>= 1.9.4), parallel, pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>=, 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
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