shazam

1.3.2

Immunoglobulin Somatic Hypermutation Analysis

2packages depend

14Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Susanna MarquezFirst published 2016-02-2124 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 18.1 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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 · 306 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 62%
Documented parameters: 100%
Return-value docs: 91%
References docs: 32%

Downloads

14K

CRAN downloads in the past year

Rank #3,347 · ~38/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

88930 days

3.6K90 days

14K1 year

Compare downloads with other packages →

Also on194 r2u36 autocran3.5K conda_forge3K bioconda

Repository

GitHub ↗ immcantation/shazam

2Stars

2Forks

9Open issues

2Open PRs

0Releases

1,382Commits

21Contributors

License AGPL-3.0 · 1,382 commits · Last activity 2026-05-26 · 0% stars, 30d

Stars over time

2025-05-23 · 12026-07-07 · 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/shazam on 2026-07-19.

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

21 external dependencies (excludes base and recommended)

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

dowser scoper

Code & Tests

Code Composition

R 12,838 (66%)Rd 5,239 (27%)Vignettes 1,315 (7%)

Code characteristics

Object systems

S4 class8S4 method9

Cyclomatic complexity: 4.0 median / 40 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

120 47 exported

Complexity

7.8 avg / 40 max

Call network

120 nodes / 130 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 1

Name	Class	Rows × Cols	Also ships in
U5N	TargetingModel	–	–

8 internal objects are bundled for the package's own use and not listed here.

People & History

People (10)

Maintainer (1)

Susanna Marquez

Author, Maintainer

Authors (9)

Susanna Marquez

Author, Maintainer

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

Contributors (1)

Ang Cui

Contributor

Steven Kleinstein

Author, Copyright holder

Package Timeline

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

1.3.2Latest
2026-05-01 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.3.1
2026-01-08 · diff ↗
1.3.0
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
2023-10-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.2
2022-10-01 · diff ↗
1.1.1
2022-05-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.0
2021-07-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.2
2020-08-11 · diff ↗
1.0.1
2020-07-19 · diff ↗
1.0.0
2020-05-11 · diff ↗

Show 20 earlier events

R
R 4.0.0 released · 2020-04-24
0.2.3
2020-02-06 · diff ↗
0.2.2
2019-12-16 · diff ↗
0.2.1
2019-07-20 · diff ↗
0.2.0
2019-07-19 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.1.11
2019-01-28 · diff ↗
0.1.10
2018-09-20 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.1.9
2018-04-01 · diff ↗
0.1.8
2017-06-30 · diff ↗
0.1.7
2017-05-14 · diff ↗
0.1.6
2017-05-13 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.1.5
2017-03-24 · diff ↗
0.1.4
2016-08-06 · diff ↗
0.1.3
2016-07-31 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.1.2
2016-02-21
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-02-21
Total releases: 24 / 10 yrs
License: AGPL-3 OSI
Minimum R: ≥ 4.0
Bundled data: 505 KB / 17 files
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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