scRecover

DOI: 10.18129/B9.bioc.scRecover    

scRecover for imputation of single-cell RNA-seq data

Bioconductor version: Release (3.9)

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 tsinghua.edu.cn>

Maintainer: Zhun Miao <miaoz13 at mails.tsinghua.edu.cn>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scRecover")

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("scRecover")

 

HTML R Script scRecover
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
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), Rmagic (>= 1.3.0), BiocParallel(>= 1.12.0)
LinkingTo
Suggests knitr, rmarkdown, SingleCellExperiment, testthat
SystemRequirements
Enhances
URL https://miaozhun.github.io/scRecover
BugReports https://github.com/miaozhun/scRecover/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scRecover_1.0.0.tar.gz
Windows Binary scRecover_1.0.0.zip
Mac OS X 10.11 (El Capitan) scRecover_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scRecover
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scRecover
Package Short Url https://bioconductor.org/packages/scRecover/
Package Downloads Report Download Stats

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