R Observatory: Metrics for SAVER version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SAVER

1.1.2Package record

Single-Cell RNA-Seq Gene Expression Recovery

0packages depend

4.6Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Mo HuangCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.1.2

Update to make compatible with glmnet 3.0.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

4NOTE9OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Mo Huang <mohuangx@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘SAVER-package.Rd’:
    https://doi.org/10.1038/s41592-018-0033-z

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘methods’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 1.4 min · r-devel-windows-x86_64

Status changes

NOTE9 OK, 4 NOTE2026-09-08
ERROR9 OK, 3 NOTE, 1 ERROR2026-09-07
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.2

READMEYes · 70 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.1.2Citation fileYes · cites a publication

Help pages: 15includes a package overview page
Examples that run: 100%6 run in a plain check
Exported functions with examples: 50%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 13%

Vignettes (1)

SAVER Tutorial

How these are measured

Downloads

4.6K

CRAN downloads in the past year

Rank #5,972 · ~13/day · ~385/mo

Releases R versions

Daily download trend is not available in this view yet.

54930 days

1.4K90 days

4.6K1 year

Compare downloads with other packages →

Also on298 r2u10 autocran1.3K conda_forge159 c2d4u

How downloads are counted

Repository

nzhanglab/SAVER ↗Account: nzhanglab

Moved from mohuangx/saver.

117Stars

20Forks

12Open issues

0Open PRs

14Releases

234Commits

4Commit identities

234 commits · Last activity 2024-11-28 · +1.7% stars, 30d · Default branch at 1.1.3, ahead of CRAN 1.1.2 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 10

Stars over time

2025-07-28 · 1102026-10-09 · 117

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/mohuangx/saver on 2026-10-11.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

GitHub Pages site last deployed 2024-11-28

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing SAVER adds 7 packages (3 with compiled code, 7.3 MB of source tarballs). Heaviest: glmnet 2.7 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Mo Huang

Author, Maintainer since 1.1.1 (2018)

Mingyao Li

Author

Nancy Zhang

Author

Releases (2)

Pick two releases to compare their code metrics.

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
record
2019-11-13 · current release · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.1
record
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

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' entry:

citation("SAVER")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1038/s41592-018-0033-z.

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 v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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