Package: SanityR 1.3.0

Teo Sakel

SanityR: R/Bioconductor interface to the Sanity model gene expression analysis

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.

Authors:Teo Sakel [aut, cre], MCIU/AEI [fnd]

SanityR_1.3.0.tar.gz
SanityR_1.3.0.zip(r-4.7)SanityR_1.3.0.zip(r-4.6)SanityR_1.3.0.zip(r-4.5)
SanityR_1.3.0.tgz(r-4.6-x86_64)SanityR_1.3.0.tgz(r-4.6-arm64)SanityR_1.3.0.tgz(r-4.5-x86_64)SanityR_1.3.0.tgz(r-4.5-arm64)
SanityR_1.3.0.tar.gz(r-4.7-arm64)SanityR_1.3.0.tar.gz(r-4.7-x86_64)SanityR_1.3.0.tar.gz(r-4.6-arm64)SanityR_1.3.0.tar.gz(r-4.6-x86_64)
SanityR_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SanityR/json (API)

# Install 'SanityR' in R:

install.packages('SanityR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/teosakel/sanityr/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:SanityR-1.3.0(bioc 3.24)SanityR-1.2.0(bioc 3.23)

software geneexpression singlecell normalization bayesian cpp

5.38 score 4 stars 6 scripts 177 downloads 4 exports 31 dependencies

Last updated from:a38d686d6c. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	171
linux-devel-arm64	NOTE	286
linux-devel-x86_64	NOTE	346
source / vignettes	OK	357
linux-release-arm64	NOTE	272
linux-release-x86_64	NOTE	357
macos-release-arm64	NOTE	227
macos-release-x86_64	NOTE	539
macos-oldrel-arm64	NOTE	265
macos-oldrel-x86_64	NOTE	453
windows-devel	NOTE	577
windows-release	NOTE	479
windows-oldrel	NOTE	462
wasm-release	OK	150

Exports:calculateSanityDistance Sanity simulate_branched_random_walk simulate_independent_cells

Dependencies:abind assorthead beachmat BH Biobase BiocGenerics BiocParallel codetools cpp11 DelayedArray formatR futile.logger futile.options generics GenomicRanges IRanges lambda.r lattice Matrix MatrixGenerics matrixStats Rcpp S4Arrays S4Vectors scuttle Seqinfo SingleCellExperiment snow SparseArray SummarizedExperiment XVector

Normalizing scRNA-seq data with Sanity

Rendered fromSanityR.Rmdusingknitr::rmarkdown

Last update: 2025-07-24
Started: 2025-05-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate the Sanity distance between samples	calculateSanityDistance
Estimate gene-level expression using the Sanity model	Sanity Sanity,ANY-method Sanity,SingleCellExperiment-method Sanity,SummarizedExperiment-method
Simulate SingleCellExperiment Datasets with Independent or Branched Gene Expression Patterns	simulate_branched_random_walk simulate_independent_cells simulate_sce