scRecover

DOI: 10.18129/B9.bioc.scRecover    

This is the development version of scRecover; for the stable release version, see scRecover.

scRecover for imputation of single-cell RNA-seq data

Bioconductor version: Development (3.17)

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 tsinghua.org.cn>

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scRecover")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.15.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 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), 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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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