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Bioconductor - scRecover (development version)

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 (3.22)

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 "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scRecover")
Details biocViews GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics Version 1.25.0 In Bioconductor since BioC 3.9 (R-3.6) (6 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 Package Archives

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

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