R Observatory: Metrics for tigger version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tigger

1.2.0

Infers Novel Immunoglobulin Alleles from Sequencing Data

2packages depend

8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

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

Infers the V genotype of an individual from immunoglobulin (Ig) repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences. Citations: Gadala-Maria, et al (2015) doi:10.1073/pnas.1417683112, Gadala-Maria, et al (2019) doi:10.3389/fimmu.2019.00129.

Changes in 1.2.0

General:

Updated dependencies to alakazam >= 1.5.0.

New Features:

Added the function plotGenotypeConfidence, which draws a genotype next to a color panel showing a per-gene confidence value, such as the k_diff returned by inferGenotypeBayesian.
Added the genotyped_alleles argument to inferGenotypeBayesian. When TRUE, a genotyped_alleles column is added with the most likely alleles based on the highest Bayesian zygosity likelihood.
Added the allele_col argument to plotGenotype to choose the column of alleles to plot (e.g., allele_col="genotyped_alleles").
Added the include_unseen and strip_d arguments to genotypeFasta. With include_unseen=TRUE, germline alleles of genes absent from the genotype are also returned. genotypeFasta now uses the genotyped_alleles column, when present, instead of alleles.

Show all changes in 1.2.0Hide the rest of the changes in 1.2.0

Added the trim_seq, overwrite, ignored_regex, treat_multigene_as_uncalled, top_k, top_by, strip_d and reassign_uncalled arguments to reassignAlleles.
reassignAlleles now supports D and J calls. The segment is determined from the prefix of the v_call argument, and the result is written to the v_call_genotyped, d_call_genotyped or j_call_genotyped column accordingly. The v_call column name must now begin with v, d or j.

Backwards Incompatible Changes:

When gene_cutoff is a fraction, inferGenotype now computes the cutoff from the number of sequences of the gene's locus instead of the whole repertoire. inferGenotype and inferGenotypeBayesian warn when calls from more than one locus are detected.

Bug Fixes:

Fixed reassignAlleles not realigning sequences when only one sequence had a gene absent from the genotype.

Performance:

reassignAlleles now uses alakazam::seqMismatchMatrix and alakazam::seqMismatchCount to compute Hamming distances, and parses allele calls only once per unique call.

From NEWS.md in the release

Install

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

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

Development version from immcantation/tigger. 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-tigger

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-tigger

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: 10.8 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 1.2.0

READMEYes · 301 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.0Citation fileYes · cites a publicationWebsiteYes

Help pages: 29 (1 internal)includes a package overview page
Examples that run: 81%17 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran) · 2 hold no code
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 95%
Help pages citing references: 31%

Vignettes (1)

Polymorphism detection and genotyping

How these are measured

Downloads

8K

CRAN downloads in the past year

Rank #4,197 · ~22/day · ~667/mo

Releases R versions

Daily download trend is not available in this view yet.

92430 days

2.1K90 days

8K1 year

Compare downloads with other packages →

Also on182 r2u8 autocran3.7K conda_forge334 bioconda

How downloads are counted

Repository

immcantation/tigger ↗Organization: immcantation

1Stars

1Forks

5Open issues

0Open PRs

0Releases

648Commits

11Commit identities

License file reads as AGPL-3.0 · 648 commits · Last activity 2026-10-09 · Default branch at 1.2.0.999, ahead of CRAN 1.2.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 10
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2026-07-07 · 02026-10-15 · 1

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/immcantation/tigger on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (2)

Code of conduct (inherited from immcantation)Contributing guide

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing tigger adds 59 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 (15)

alakazam dplyr doParallel foreachgraphicsgridExtra gtools iterators lazyevalparallelrlangstatsstringi tidyrutils

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Depends, Imports or LinkingTo, most downloaded first

ogrdbstats piglet

How these are counted

Code & Tests

Datasets

People & History

People (7)

Susanna Marquez

Author, Maintainer since 1.0.1 (2022) · added in 0.3.0

Moriah Cohen

Author · added in 0.3.0

Daniel Gadala-Maria

Author

Steven Kleinstein

Author, Copyright holder

Ayelet Peres

Author · added in 1.1.3

Jason Vander Heiden

Author

Gur Yaari

Author · added in 0.3.0

Previously maintained by Jason Vander Heiden (0.2.10 to 1.0.0) and Daniel Gadala-Maria (0.2.5 to 0.2.9.999).

Releases (15)

Pick two releases to compare their code metrics.

1.2.0Latest
record
2026-10-06 · current release · diff ↗ ·
added 1 export
plotGenotypeConfidence
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R 4.6.0 released · 2026-04-24
1.1.3
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2026-04-17 · diff ↗
1.1.2
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2026-01-10 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.0
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2023-10-10 · diff ↗
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R 4.3.0 released · 2023-04-21
1.0.1
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2022-09-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.0
record
2020-05-13 · diff ↗ ·
added 1 export
subsampleDb
R
R 4.0.0 released · 2020-04-24
0.4.0
record
2019-07-19 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3.1
record
2018-10-19 · diff ↗

Show 10 earlier eventsHide 10 earlier events

0.3.0
record
2018-10-03 · diff ↗ ·
added 2 exports
generateEvidence, inferGenotypeBayesian
R
R 3.5.0 released · 2018-04-23
0.2.11
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2017-09-21 · diff ↗
0.2.10
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2017-07-03 · diff ↗
0.2.9.999
record
2017-05-16 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.2.8
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2016-08-28 · diff ↗
0.2.7
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2016-07-25 · diff ↗
0.2.5
record
2016-06-08
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-06-08
Total releases: 15 / 10 yrs
License: AGPL-3 OSI · relicensed from CC BY-SA 4.0 in 1.0.0
Minimum R: ≥ 4.0
Bundled data: 2.5 MB / 6 files
Download size: 2.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("tigger")

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

It points to 10.1073/pnas.1417683112, 10.3389/fimmu.2019.00129.

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 tigger version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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