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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| scRecover | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | scRecover_1.29.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | scRecover_1.29.0.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 |