scRecover

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see scRecover.

scRecover for imputation of single-cell RNA-seq data


Bioconductor version: 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 (!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 1.0.0
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), Rmagic (>= 1.3.0), 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/scRecover/
Package Short Url https://bioconductor.org/packages/scRecover/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive