R Observatory: Metrics for SCIBER version 0.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SCIBER

0.2.2Package record

Single-Cell Integrator and Batch Effect Remover

0packages depend

2.4Kdownloads / year

81.2%test coverage

13/13flavors OK

Overview

About

Maintained by Dailin GanCRAN page ↗GitHub ↗Issues ↗

Remove batch effects by projecting query batches into the reference batch space.

Install

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

install.packages("SCIBER", 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("RavenGan/SCIBER")

Development version from RavenGan/SCIBER. 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-sciber

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-SCIBER

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-SCIBER

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

13OK

CRAN check page ↗

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.2

READMEYes · 301 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 2
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Quick start to SCIBER HTML

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #18,719 · ~7/day · ~200/mo

Releases R versions

Daily download trend is not available in this view yet.

27430 days

69290 days

2.4K1 year

Compare downloads with other packages →

Also on69 r2u9 autocran

How downloads are counted

Repository

ravengan/sciber ↗Account: RavenGan

4Stars

1Forks

4Open issues

0Open PRs

0Releases

52Commits

1Commit identities

52 commits · Last activity 2023-05-02 · 0% stars, 30d · The default branch showed an older version (0.2.1) than CRAN on 2026-10-18

Responsiveness

not measured

Stars over time

2023-08-05 · 42026-07-07 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/ravengan/sciber on 2026-10-18.

Docs source (1)

README.Rmd

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing SCIBER adds 15 packages (9 with compiled code, 5.2 MB of source tarballs). Heaviest: vctrs 1.0 MB, dplyr 902 KB, rlang 766 KB.

Depends (1)

R >= 2.10

Imports (3)

dplyrparallelstats

LinkingTo (0)

none

Suggests (8)

knitr rmarkdown testthat cowplot ggplot2 ggthemesMatrixuwot

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 (2)

Dailin Gan

Author, Maintainer since 0.1.1 (2022)

Jun Li

Author

Releases (7)

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
0.2.2Latest
record
2023-05-02 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.6
record
2023-02-09 · diff ↗
0.1.5
record
2022-07-17 · diff ↗
0.1.4
record
2022-07-14 · diff ↗
0.1.3
record
2022-07-06 · diff ↗
0.1.2
record
2022-06-22 · diff ↗ ·
removed 1 export
SCIBER_int

added 1 export
SCIBER
0.1.1
record
2022-04-28
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-04-28
Total releases: 7 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 509 KB / 1 file
Download size: 594 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SCIBER")

Format

Gan, D., & Li, J. (2023). SCIBER: Single-Cell Integrator and Batch Effect Remover (Version 0.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.SCIBER

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 SCIBER version 0.2.2 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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