DOI: 10.18129/B9.bioc.scRecover  

scRecover for imputation of single-cell RNA-seq data

Bioconductor version: Release (3.18)

scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.

Author: Zhun Miao, Xuegong Zhang <zhangxg at>

Maintainer: Zhun Miao <miaoz13 at>

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


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biocViews GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License GPL
Depends R (>= 3.4.0)
Imports stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel(>= 1.12.0)
Suggests knitr, rmarkdown, SingleCellExperiment, testthat
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