Registration Open for EuroBioC2025:
European Bioconductor Conference!

SanityR

This is the development version of SanityR; to use it, please install the devel version of Bioconductor.

R/Bioconductor interface to the Sanity model gene expression analysis


Bioconductor version: Development (3.22)

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] ORCID iD ORCID: 0000-0001-9946-9498 , MCIU/AEI [fnd] (ROR: <https://ror.org/05r0vyz12>, DOI: 10.13039/501100011033)

Maintainer: Teo Sakel <teo at intelligentbiodata.com>

Citation (from within R, enter citation("SanityR")):

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("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 PDF

Details

biocViews Bayesian, GeneExpression, Normalization, SingleCell, Software
Version 0.99.3
In Bioconductor since BioC 3.22 (R-4.5)
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_0.99.3.tar.gz
Windows Binary (x86_64) SanityR_0.99.3.zip
macOS Binary (x86_64) SanityR_0.99.3.tgz
macOS Binary (arm64) SanityR_0.99.3.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