R Observatory: Metrics for scoper version 1.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scoper

1.6.0Package record

Spectral Clustering-Based Method for Identifying B Cell Clones

0packages depend

8.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Susanna MarquezCRAN page ↗GitHub ↗Website ↗Issues ↗

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>.

Changes in 1.6.0

General:

Increased required version of alakazam to >= 1.5.0. hierarchicalClones now uses alakazam's C++ Hamming distance implementations (fastDist, fastDistAA) and passes their dist output directly to hclust, reducing memory usage for large VJL groups when IUPAC=FALSE.

Clonal analysis:

hierarchicalClones and identicalClones now allow amino acid junction sequences if method="aa". Previously, the junction column was always assumed to hold nucleotide sequences and translated before clustering.
Added a junction_type argument ("auto", "nt", "aa") to identicalClones, hierarchicalClones, and defineClonesScoper. It lets users declare whether junction holds nucleotide or amino acid content when method="aa", instead of relying on auto detection, which cannot reliably tell apart short amino acid junctions made only of letters shared with the nucleotide alphabet (e.g. "CARDST").

Show all changes in 1.6.0Hide the rest of the changes in 1.6.0

Expanded the IUPAC parameter in hierarchicalClones to both method="nt" and method="aa".
Improved clonal clustering speed with a new Alakazam C++ Hamming distance implementation for amino acid sequences (fastDistAA) if method="aa" and IUPAC=FALSE (default).

Bug fixes:

Fixed identicalClones with method="aa": translated amino acid junctions were computed but never used for grouping, so clustering was actually based on the untranslated nucleotide sequences, incorrectly splitting synonymous junctions into separate clones.
Fixed identicalClones, hierarchicalClones, and spectralClones in single-cell mode with summarize_clones=TRUE: vjl_groups and inter_intra could reference clone_id values no longer matching those in db, due to clone ids being renumbered again after merging light chain data without updating those summaries. (Issue #52)
Updated how scoper decides whether the junction/cdr3 column holds nucleotide or amino acid sequences. The decision is now made once per dataset. mod3=TRUE is now ignored (with a warning) for amino acid junctions, since length says nothing about reading frame for amino acids. A warning is also issued when method="aa" is set but no sequence in the data can be confirmed as amino acid.

From NEWS.md in the release

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. 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

# 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). 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: 10.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
ERROR13 OK, 1 ERROR2026-03-30
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.0

READMEYes · 114 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.6.0Citation fileYes · cites a publicationWebsiteYes

Help pages: 8 (1 internal)includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 25%

Vignettes (1)

Inferring B cell clonal relationships

How these are measured

Downloads

8.4K

CRAN downloads in the past year

Rank #4,155 · ~23/day · ~697/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

2.1K90 days

8.4K1 year

Compare downloads with other packages →

Also on534 r2u8 autocran2K bioconda

How downloads are counted

Repository

immcantation/scoper ↗Organization: immcantation

0Stars

3Forks

3Open issues

0Open PRs

0Releases

535Commits

13Commit identities

License file reads as AGPL-3.0 · 535 commits · Last activity 2026-10-05 · Default branch at 1.6.0.999, ahead of CRAN 1.6.0 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 85%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 2

Issues over time

2026-07-14 · 32026-10-01 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/immcantation/scoper on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (3)

Code of conduct (inherited from immcantation)Contributing guideIssue templates

Reproducibility and dev environment (2)

data-raw/Dev Container

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing scoper adds 61 packages (35 with compiled code, 62 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 3 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (9)

Susanna Marquez

Contributor, Maintainer since 1.2.1 (2022) · added in 1.2.1

Steven Kleinstein

Author, Copyright holder

Nima Nouri

Author

Jason Vander Heiden

Author

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

Previously maintained by Jason Vander Heiden (1.0.0 to 1.2.0) and Nima Nouri (0.1.0 to 0.2.0).

Releases (11)

Pick two releases to compare their code metrics.

1.6.0Latest
record
2026-10-04 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-04 20:43 UTC, so it stayed less than the time between readings.
1.5.0
record
2026-05-05 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.4.0
record
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
record
2023-10-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.1
record
2022-09-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
record
2021-11-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.1.0
record
2020-08-10 · diff ↗
1.0.1
record
2020-05-25 · diff ↗
1.0.0
record
2020-05-17 · diff ↗ ·
removed 1 export
defineClonesScoper

added 4 exports
hierarchicalClones, identicalClones, plotCloneSummary, spectralClones
R
R 4.0.0 released · 2020-04-24

Show 4 earlier eventsHide 4 earlier events

0.2.0
record
2019-08-05 · diff ↗ ·
removed 1 export
analyzeClones
R
R 3.6.0 released · 2019-04-26
0.1.0
record
2018-10-14
R
R 3.5.0 released · 2018-04-23

Across CRAN, the median accepted release of the past year spent 23 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2018-10-14
Total releases: 11 / 8 yrs
License: AGPL-3 OSI · relicensed from CC BY-SA 4.0 in 1.0.0
Minimum R: ≥ 4.0
Bundled data: 96 KB / 1 file
Download size: 397 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("scoper")

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

It points to 10.1093/bioinformatics/bty235, 10.1371/journal.pcbi.1007977, 10.4049/jimmunol.1601850.

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 1.6.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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