R Observatory: Metrics for scoper version 1.5.0

Balamuta, James Joseph

scoper

1.5.0

Spectral Clustering-Based Method for Identifying B Cell Clones

0packages depend

8.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Susanna MarquezFirst published 2018-10-1410 releasesCRAN page ↗GitHub ↗

Provides a computational framework for identification of B cell clones from Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main functions are included (identicalClones, hierarchicalClones, and spectralClones) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>. Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>. Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.

Install

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

install.packages("scoper", 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("immcantation/scoper")

Development version from immcantation/scoper. 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-scoper

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

# 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-scoper

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

Health

CRAN checks

13OK

Slowest check: 11.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

15

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 114 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 25%

Downloads

8.4K

CRAN downloads in the past year

Rank #4,718 · ~23/day · ~697/mo

Releases R versions

Daily download trend is not available in this view yet.

41030 days

1.7K90 days

8.4K1 year

Compare downloads with other packages →

Also on548 r2u6 autocran1.9K bioconda

Repository

GitHub ↗ immcantation/scoper

0Stars

3Forks

2Open issues

2Open PRs

0Releases

497Commits

13Contributors

License AGPL-3.0 · 497 commits · Last activity 2026-08-06

Issues over time

2026-07-14 · 32026-08-06 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/immcantation/scoper on 2026-08-03.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

data-raw/Dev Container

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.0ggplot2

Imports (14)

alakazam shazam data.table doParallel dplyr fastcluster foreachmethodsRcpp rlang scalesstatsstringi tidyr

LinkingTo (1)

Rcpp

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

Susanna Marquez

Contributor, Maintainer · added in 1.2.1

Authors (3)

Steven Kleinstein

Author, Copyright holder

Nima Nouri

Author

Jason Vander Heiden

Author

Contributors (6)

Susanna Marquez

Contributor, Maintainer · added in 1.2.1

Edel Aron

Contributor · added in 1.0.0

Robert Bjornson

Contributor · added in 1.5.0

Gisela Gabernet

Contributor · added in 1.3.0

Cole Jensen

Contributor · added in 1.4.0

Huimin Lyu

Contributor · added in 1.4.0

Copyright holders (1)

Steven Kleinstein

Author, Copyright holder

Package Timeline

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

1.5.0Latest
2026-05-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.4.0
2026-01-08 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.3.0
2023-10-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.1
2022-09-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
2021-11-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.1.0
2020-08-10 · diff ↗
1.0.1
2020-05-25 · diff ↗
1.0.0
2020-05-17 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.2.0
2019-08-05 · diff ↗

Show 3 earlier events

R
R 3.6.0 released · 2019-04-26
0.1.0
2018-10-14
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-10-14
Total releases: 10 / 8 yrs
License: AGPL-3 OSI
Minimum R: ≥ 4.0
Bundled data: 96 KB / 1 file
Download size: 388 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scoper")

Format

Marquez, S., Aron, E., Bjornson, R., Gabernet, G., Jensen, C., Kleinstein, S., Lyu, H., Nouri, N., & Vander Heiden, J. (2026). scoper: Spectral Clustering-Based Method for Identifying B Cell Clones (Version 1.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.scoper

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 scoper version 1.5.0 [Data set]. HJJB, LLC. Data release v2026-08-07. https://r-observatory.thecoatlessprofessor.com/packages/scoper

From data release v2026-08-07, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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