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("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 | ||
| 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 |