R Observatory: Metrics for SAVER version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SAVER

1.1.2

Single-Cell RNA-Seq Gene Expression Recovery

0packages depend

5.1Kdownloads / year

–test coverage

9/13checks pass

Overview

About

Maintained by Mo HuangFirst published 2018-10-142 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("SAVER", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("mohuangx/SAVER")

Development version from mohuangx/SAVER. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-saver

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SAVER

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SAVER

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

4NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

NOTE2026-03-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 70 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 100%
References docs: 13%

Downloads

5.1K

CRAN downloads in the past year

Rank #8,158 · ~14/day · ~423/mo

Releases R versions

Daily download trend is not available in this view yet.

29930 days

1.1K90 days

5.1K1 year

Compare downloads with other packages →

Also on230 r2u17 autocran1.3K conda_forge72 c2d4u

Repository

GitHub ↗ mohuangx/saver

115Stars

20Forks

12Open issues

0Open PRs

14Releases

234Commits

4Contributors

234 commits · Last activity 2024-11-28 · -0.9% stars, 30d

Stars over time

2025-07-28 · 1102026-07-30 · 115

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/mohuangx/saver on 2026-08-09.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.1

Imports (6)

glmnet foreachmethodsiterators doParallelMatrix

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Mo Huang

Author, Maintainer

Authors (3)

Mo Huang

Author, Maintainer

Mingyao Li

Author

Nancy Zhang

Author

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.1.2Latest
2019-11-13 · current release · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.1
2018-10-14
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-10-14
Total releases: 2 / 8 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.0.1
Bundled data: 2.8 MB / 3 files
Download size: 2.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SAVER")

Format

Huang, M., Li, M., & Zhang, N. (2019). SAVER: Single-Cell RNA-Seq Gene Expression Recovery (Version 1.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.SAVER

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SAVER version 1.1.2 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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