Package: SAVER 1.1.3

SAVER: Single-Cell RNA-Seq Gene Expression Recovery

An implementation of a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. See Huang M, et al (2018) <doi:10.1038/s41592-018-0033-z> for more details.

Authors:Mo Huang [aut, cre], Nancy Zhang [aut], Mingyao Li [aut]

SAVER_1.1.3.tar.gz
SAVER_1.1.3.zip(r-4.7)SAVER_1.1.3.zip(r-4.6)SAVER_1.1.3.zip(r-4.5)
SAVER_1.1.3.tgz(r-4.6-any)SAVER_1.1.3.tgz(r-4.5-any)
SAVER_1.1.3.tar.gz(r-4.7-any)SAVER_1.1.3.tar.gz(r-4.6-any)
SAVER_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SAVER/json (API)
NEWS

# Install 'SAVER' in R:

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

Bug tracker:https://github.com/mohuangx/saver/issues

Datasets:

linnarsson - Mouse brain single-cell RNA-seq dataset
linnarsson_saver - SAVER recovered mouse brain single-cell RNA-seq dataset

On CRAN:

8.99 score 114 stars 2 packages 283 scripts 320 downloads 40 mentions 21 exports 11 dependencies

Last updated from:f28d719c1b. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	93
source / vignettes	OK	161
linux-release-x86_64	OK	112
macos-release-arm64	OK	161
macos-oldrel-arm64	OK	173
windows-devel	OK	88
windows-release	OK	88
windows-oldrel	OK	74
wasm-release	OK	104

Exports:calc.a calc.b calc.estimate calc.estimate.mean calc.estimate.null calc.k calc.loglik.a calc.loglik.b calc.loglik.k calc.maxcor calc.post combine.saver cor.cells cor.genes expr.predict get.mu sample.saver saver saver.fit saver.fit.mean saver.fit.null

Dependencies:codetools doParallel foreach glmnet iterators lattice Matrix Rcpp RcppEigen shape survival

SAVER Tutorial

Rendered fromsaver-tutorial.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2022-06-13
Started: 2018-08-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
SAVER: Single-cell Analysis Via Expression Recovery	SAVER-package
Optimizes variance	calc.a calc.b calc.k
Calculate estimate	calc.estimate calc.estimate.mean calc.estimate.null
Calculates marginal likelihood	calc.loglik.a calc.loglik.b calc.loglik.k
Calculate maximum correlation	calc.maxcor
Calculates SAVER posterior	calc.post
Combines SAVER	combine.saver
Calculates gene-to-gene and cell-to-cell SAVER correlation	cor.cells cor.genes
Calculates SAVER prediction.	expr.predict
Output prior predictions	get.mu
Mouse brain single-cell RNA-seq dataset	linnarsson
SAVER recovered mouse brain single-cell RNA-seq dataset	linnarsson_saver
Samples from SAVER	sample.saver
Runs SAVER	saver
Fits SAVER	saver.fit saver.fit.mean saver.fit.null