SanityR
This is the development version of SanityR; for the stable release version, see SanityR.
R/Bioconductor interface to the Sanity model gene expression analysis
Bioconductor version: Development (3.24)
a Bayesian normalization procedure derived from first principles. Sanity estimates expression values and associated error bars directly from raw unique molecular identifier (UMI) counts without any tunable parameters.
Author: Teo Sakel [aut, cre]
, MCIU/AEI [fnd] (ROR: <https://ror.org/05r0vyz12>, DOI: 10.13039/501100011033)
Maintainer: Teo Sakel <teo at intelligentbiodata.com>
citation("SanityR")):
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("SanityR")
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("SanityR")| Normalizing scRNA-seq data with Sanity | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, GeneExpression, Normalization, SingleCell, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | GPL (>= 3) |
| Depends | |
| Imports | Rcpp, BiocGenerics, BiocParallel, MatrixGenerics, methods, S4Vectors, scuttle, SingleCellExperiment, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/TeoSakel/SanityR |
| Bug Reports | https://github.com/TeoSakel/SanityR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), scater, Rtsne |
| Linking To | Rcpp |
| 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 | SanityR_1.3.0.tar.gz |
| Windows Binary (x86_64) | SanityR_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | SanityR_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | SanityR_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SanityR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SanityR |
| Bioc Package Browser | https://code.bioconductor.org/browse/SanityR/ |
| Package Short Url | https://bioconductor.org/packages/SanityR/ |
| Package Downloads Report | Download Stats |