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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 tsinghua.edu.cn>

Maintainer: Zhun Miao <miaoz13 at tsinghua.org.cn>

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

Installation

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


if (!require("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")
scRecover HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (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)
System Requirements
URL https://miaozhun.github.io/scRecover
Bug Reports https://github.com/miaozhun/scRecover/issues
See More
Suggests knitr, rmarkdown, SingleCellExperiment, testthat
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Build Report Build Report

Package Archives

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

Source Package scRecover_1.18.0.tar.gz
Windows Binary scRecover_1.18.0.zip
macOS Binary (x86_64) scRecover_1.18.0.tgz
macOS Binary (arm64) scRecover_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scRecover
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scRecover
Bioc Package Browser https://code.bioconductor.org/browse/scRecover/
Package Short Url https://bioconductor.org/packages/scRecover/
Package Downloads Report Download Stats