scRecover
This is thereleased version of scRecover; for the devel version, seescRecover.
scRecover for imputation of single-cell RNA-seq data
Bioconductor version: Release (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("scRecover")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("scRecover")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression,Preprocessing,RNASeq,Sequencing,SingleCell,Software,Transcriptomics |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | scRecover_1.26.0.tar.gz |
| Windows Binary (x86_64) | scRecover_1.26.0.zip |
| macOS Binary (x86_64) | scRecover_1.26.0.tgz |
| macOS Binary (arm64) | scRecover_1.26.0.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 |