R Observatory: Metrics for alakazam version 1.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

alakazam

1.5.0Package record

Immunoglobulin Clonal Lineage and Diversity Analysis

8packages dependsuggested by 1

24.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

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

Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) doi:10.1093/bioinformatics/btv359, Stern, Yaari and Vander Heiden, et al (2014) doi:10.1126/scitranslmed.3008879.

Changes in 1.5.0

Sequence:

Added fastDist, a faster calculation of pairwise Hamming distances for DNA sequences of equal length containing only the characters ACTGN?.
Added fastDistAA, a faster calculation of pairwise distances for amino acid sequences of equal length.
Added seqMismatchCount, seqMismatchMatrix and seqMismatchPositions to count, tabulate and locate mismatches between sample and germline sequences.
Added the fields argument to collapseDuplicates, specifying columns (e.g. c_call) whose values must match for sequences to be collapsed together.
Fixed the ignore argument of collapseDuplicates, which was never used. Sequence equality was always tested with the default c("N", "-", ".", "?").

Show all changes in 1.5.0Hide the rest of the changes in 1.5.0

Added the ignore argument to pairwiseEqual, which previously always used the seqEqual default of c("N", "-", ".", "?").

From NEWS.md in the release

Install

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

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

Development version from immcantation/alakazam. 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-alakazam

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-alakazam

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-alakazam

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: 15.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
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 1.5.0

READMEYes · 200 wordsVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 1.5.0Citation fileYes · cites a publicationWebsiteYes

Help pages: 84 (1 internal)includes a package overview page
Examples that run: 79%53 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 10 never run
Exported functions with examples: 93%
Documented parameters: 98%
Return-value docs: 92%
Help pages citing references: 30%

Vignettes (5)

How these are measured

Downloads

24.1K

CRAN downloads in the past year

Rank #2,676 · ~66/day · ~2K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.4K30 days

5.8K90 days

24.1K1 year

Compare downloads with other packages →

Also on884 r2u20 autocran5.1K conda_forge2.5K bioconda

How downloads are counted

Repository

immcantation/alakazam ↗Organization: immcantation

3Stars

6Forks

7Open issues

1Open PRs

0Releases

1,252Commits

27Commit identities

License file reads as AGPL-3.0 · 1,252 commits · Last activity 2026-10-15 · 0% stars, 30d · Default branch at 1.5.0.999, ahead of CRAN 1.5.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 58
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-07-21 · 12026-07-07 · 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/alakazam on 2026-10-21.

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 v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-09-30
Pull request: opened by its own account
Commits: 2 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

22 external dependencies (excludes base and recommended)

Installing alakazam adds 52 packages (30 with compiled code, 52 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 (22)

airr ape dplyrgraphicsgridigraphMatrixmethodsprogress Rcpp (>= 0.12.12)readr rlang scales seqinrstatsstringi tibble tidyrutilsBiostrings GenomicAlignments IRanges

LinkingTo (1)

Rcpp

Suggests (4)

cigarillo knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

8direct

1indirect

Imports 8

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

shazam scoper tigger dowser UniprotR AbSolution piglet ogrdbstats

Suggests, most downloaded first

AntibodyForests

How these are counted

Code & Tests

Datasets

People & History

People (16)

Susanna Marquez

Maintainer since 1.3.0 (2023), Author

Namita Gupta

Author

Kenneth Hoehn

Author · added in 0.3.0

Cole Jensen

Author · added in 1.3.0

Ruoyi Jiang

Author · added in 0.2.11

Steven Kleinstein

Author, Copyright holder · added in 0.2.3

Nima Nouri

Author · added in 0.2.10

Jason Vander Heiden

Author

Julian Zhou

Author · added in 0.3.0

Edel Aron

Contributor · added in 1.1.0

Gisela Gabernet

Contributor · added in 1.4.0

Daniel Gadala-Maria

Contributor

Huimin Lyu

Contributor · added in 1.4.2

Hailong Meng

Contributor · added in 1.4.0

Burhan Sabuwala

Contributor · added in 1.4.0

Caroline Sullivan

Contributor · added in 1.4.0

Previously maintained by Jason Vander Heiden (0.2.2 to 1.2.1).

Listed in earlier versions (2)

Roy Jiang

no longer listed · 0.2.2 to 0.2.9

Rouyi Jiang

no longer listed · 0.2.10

Releases (23)

Pick two releases to compare their code metrics.

1.5.0Latest
record
2026-09-28 · current release · diff ↗ ·
added 5 exports
fastDist, fastDistAA, seqMismatchCount, seqMismatchMatrix, seqMismatchPositions
1.4.3
record
2026-04-29 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.4.2
record
2025-12-16 · diff ↗
1.4.1
record
2025-10-02 · diff ↗
1.4.0
record
2025-09-25 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.3.0
record
2023-09-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.1
record
2022-09-21 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
record
2021-11-01 · diff ↗ ·
added 1 export
junctionAlignment
R
R 4.1.0 released · 2021-05-18
1.1.0
record
2021-02-07 · diff ↗ ·
added 6 exports
DNA_IUPAC, getChain, getLocus, getPositionQuality, maskPositionsByQuality, readFastqDb
1.0.2
record
2020-07-19 · diff ↗

Show 19 earlier eventsHide 19 earlier events

1.0.1
record
2020-05-11 · diff ↗
1.0.0
record
2020-05-08 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.3.0
record
2019-07-18 · diff ↗ ·
added 5 exports
alphaDiversity, combineIgphyml, graphToPhylo, phyloToGraph, readIgphyml
R
R 3.6.0 released · 2019-04-26
0.2.11
record
2018-09-14 · diff ↗ ·
added 6 exports
baseTheme, checkColumns, cpuCount, groupGenes, nonsquareDist, progressBar
R
R 3.5.0 released · 2018-04-23
0.2.10
record
2018-03-30 · diff ↗
0.2.9
record
2018-03-22 · diff ↗ ·
removed 1 export
plotAbundance

added 3 exports
padSeqEnds, plotAbundanceCurve, plotDiversityTest
0.2.8
record
2017-09-21 · diff ↗
0.2.7
record
2017-06-15 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.2.6
record
2017-03-23 · diff ↗
0.2.5
record
2016-08-06 · diff ↗
0.2.4
record
2016-07-29 · diff ↗ ·
removed 4 exports
getSeqDistance, getSeqMatrix, multiggplot, testSeqEqual

added 16 exports
getMRCA, getPathLengths, gridPlot, pairwiseDist, pairwiseEqual, permuteLabels, plotEdgeTest, plotMRCATest, plotSubtrees, seqDist, seqEqual, sortGenes, summarizeSubtrees, tableEdges, testEdges, testMRCA
R
R 3.3.0 released · 2016-05-03
0.2.3
record
2016-02-22 · diff ↗
0.2.2
record
2016-01-29
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-01-29
Total releases: 23 / 10 yrs
License: AGPL-3 OSI · relicensed from CC BY-SA 4.0 in 1.0.0
Minimum R: ≥ 4.0
Bundled data: 298 KB / 5 files
Download size: 1.5 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("alakazam")

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

It points to 10.1093/bioinformatics/btv359, 10.1126/scitranslmed.3008879.

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 alakazam version 1.5.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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