R Observatory: Metrics for shazam version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

shazam

1.4.0Package record

Immunoglobulin Somatic Hypermutation Analysis

2packages depend

14Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

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

Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) doi:10.1093/bioinformatics/btv359, Yaari, et al (2012) doi:10.1093/nar/gks457, Yaari, et al (2013) doi:10.3389/fimmu.2013.00358, Cui, et al (2016) doi:10.4049/jimmunol.1502263.

Changes in 1.4.0

Backwards Incompatible Changes:

Removed the unused cloneColumn argument from observedMutations(), expectedMutations(), and calcBaseline(). Calls that still pass cloneColumn will now fail with an "unused argument" error and must drop the argument. Results are unchanged, as the argument was never used.

Distance Profiling:

findThreshold(method="gmm") results can now be reproduced by calling set.seed() beforehand. Previously, the fitting procedure reset the random number generator internally, so results differed between runs and the caller's random number generator state was overwritten.
Improved the speed and memory usage of distToNearest() when assigning sequences to groups.

Show all changes in 1.4.0Hide the rest of the changes in 1.4.0

Targeting Models:

Fixed the built-in U5N targeting model, which was missing the numMutS and numMutR slots and would error (no slot of name "numMutS"...) on any operation reading those slots. Model values are unchanged.

From NEWS.md in the release

Install

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

install.packages("shazam", 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/shazam")

Development version from immcantation/shazam. 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-shazam

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-shazam

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: 15.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-03-30
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.0

READMEYes · 306 wordsVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 1.4.0Citation fileYes · cites a publicationWebsiteYes

Help pages: 66 (1 internal)includes a package overview page
Examples that run: 62%29 run in a plain check · 15 only when donttest examples are enabled (R CMD check --as-cran) · 3 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 91%
Help pages citing references: 32%

Vignettes (5)

How these are measured

Downloads

14K

CRAN downloads in the past year

Rank #3,419 · ~38/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

3.2K90 days

14K1 year

Compare downloads with other packages →

Also on306 r2u9 autocran3.5K conda_forge3.2K bioconda

How downloads are counted

Repository

immcantation/shazam ↗Organization: immcantation

3Stars

3Forks

5Open issues

1Open PRs

0Releases

1,427Commits

21Commit identities

License file reads as AGPL-3.0 · 1,427 commits · Last activity 2026-10-04 · 0% stars, 30d · Default branch at 1.4.0.999, ahead of CRAN 1.4.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 34
Median days to close, 50 most recently updated closed PRs: 5

Stars over time

2025-05-23 · 12026-09-12 · 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/shazam on 2026-10-11.

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)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-12-12
Pull request: opened by its own account
Commits: 4 by its own account

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing shazam adds 58 packages (33 with compiled code, 55 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB. 3 more not on CRAN are not measured.

Depends (2)

R >= 4.0ggplot2

Imports (24)

alakazam ape diptest doParallel dplyr foreachgraphicsgridigraph iteratorsKernSmoothlazyevalMASSmethodsparallelprogress rlang scales seqinrstatsstringi tidyr tidyselectutils

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Depends, Imports or LinkingTo, most downloaded first

dowser scoper

How these are counted

Code & Tests

Datasets

People & History

People (10)

Susanna Marquez

Author, Maintainer since 1.2.0 (2023)

Namita Gupta

Author

Steven Kleinstein

Author, Copyright holder

Nima Nouri

Author · added in 0.1.5

Author

Author

Author

Author · added in 1.2.0

Julian Zhou

Author · added in 0.1.3

Ang Cui

Contributor

Previously maintained by Jason Vander Heiden (0.1.2 to 1.1.2).

Releases (25)

Pick two releases to compare their code metrics.

1.4.0Latest
record
2026-10-01 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.3.2
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2026-01-08 · diff ↗
1.3.1
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2026-01-08 · diff ↗
1.3.0
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2025-10-20 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.0
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2023-10-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.2
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2022-10-01 · diff ↗ ·
added 1 export
plotSlideWindowTune
1.1.1
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2022-05-24 · diff ↗ ·
added 1 export
convertNumbering
R
R 4.2.0 released · 2022-04-22
1.1.0
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2021-07-09 · diff ↗ ·
added 2 exports
makeGraphDf, setRegionBoundaries
R
R 4.1.0 released · 2021-05-18
1.0.2
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2020-08-11 · diff ↗
1.0.1
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2020-07-19 · diff ↗

Show 21 earlier eventsHide 21 earlier events

1.0.0
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2020-05-11 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.2.3
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2020-02-06 · diff ↗
0.2.2
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2019-12-16 · diff ↗
0.2.1
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2019-07-20 · diff ↗
0.2.0
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2019-07-19 · diff ↗ ·
added 1 export
consensusSequence
R
R 3.6.0 released · 2019-04-26
0.1.11
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2019-01-28 · diff ↗
0.1.10
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2018-09-20 · diff ↗ ·
removed 3 exports
clearConsole, getPlatform, getnproc
R
R 3.5.0 released · 2018-04-23
0.1.9
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2018-04-01 · diff ↗ ·
removed 1 export
getBaselineStats

added 1 export
calculateMutability
0.1.8
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2017-06-30 · diff ↗
0.1.7
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2017-05-14 · diff ↗
0.1.6
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2017-05-13 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.1.5
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2017-03-24 · diff ↗ ·
added 15 exports
editBaseline, findThreshold, makeAverage1merMut, makeAverage1merSub, makeDegenerate5merMut, makeDegenerate5merSub, minNumMutationsTune, minNumSeqMutationsTune, plotDensityThreshold, plotGmmThreshold, plotTune, slideWindowDb, slideWindowSeq, slideWindowTune, slideWindowTunePlot
0.1.4
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2016-08-06 · diff ↗
0.1.3
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2016-07-31 · diff ↗ ·
removed 3 exports
calcDBExpectedMutations, calcDBObservedMutations, collapseByClone

added 6 exports
collapseClones, expectedMutations, observedMutations, shmulateSeq, shmulateTree, testBaseline
R
R 3.3.0 released · 2016-05-03
0.1.2
record
2016-02-21
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-02-21
Total releases: 25 / 10 yrs
License: AGPL-3 OSI · relicensed from CC BY-SA 4.0 in 1.0.0
Minimum R: ≥ 4.0
Bundled data: 464 KB / 17 files
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("shazam")

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

It points to 10.1093/bioinformatics/btv359, 10.1093/nar/gks457, 10.3389/fimmu.2013.00358, 10.4049/jimmunol.1502263, 10.3389/fimmu.2018.01687.

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 shazam version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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