R Observatory: Metrics for immunarch version 0.10.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

immunarch

0.10.3

Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R

0packages depend

16.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Vadim I. NazarovFirst published 2020-05-1311 releasesCRAN page ↗GitHub ↗

A comprehensive analytics framework for building reproducible pipelines on T-cell and B-cell immune receptor repertoire data. Delivers multi-modal immune profiling (bulk, single-cell, CITE-seq/AbSeq, spatial, immunogenicity data), feature engineering (ML-ready feature tables and matrices), and biomarker discovery workflows (cohort comparisons, longitudinal tracking, repertoire similarity, enrichment). Provides a user-friendly interface to widely used AIRR methods — clonality/diversity, V(D)J usage, similarity, annotation, tracking, and many more. Think Scanpy or Seurat, but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or VDJ sequencing data. A successor to our previously published "tcR" R package (Nazarov 2015).

Install

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

install.packages("immunarch", 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("immunomind/immunarch")

Development version from immunomind/immunarch. 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-immunarch

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

# 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-immunarch

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-immunarch

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 7.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

37

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 8 earlier snapshots

ERROR2026-05-17
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-13
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-21
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
5 OK · 2 NOTE · 0 WARNING · 7 ERROR · 0 FAILURE

Documentation

READMEYes · 1,121 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 52%
Documented parameters: 92%
Return-value docs: 98%
References docs: 0%

Downloads

16.8K

CRAN downloads in the past year

Rank #3,639 · ~46/day · ~1.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

70530 days

2.6K90 days

16.8K1 year

Compare downloads with other packages →

Also on664 r2u20 autocran4.1K conda_forge23 c2d4u

Repository

GitHub ↗ immunomind/immunarch

341Stars

71Forks

12Open issues

1Open PRs

21Releases

739Commits

13Contributors

immunomicsdata-sciencebioinformaticsimmune-repertoireairrimmunotherapyvaccinebiomarker-discovery

License Apache-2.0 · 739 commits · Last activity 2026-08-14 · +0.6% stars, 30d

Stars over time

2025-07-14 · 3172026-08-10 · 341

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/immunomind/immunarch on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Dockerfile

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

56 external dependencies (excludes base and recommended)

Depends (4)

R >= 4.2.0ggplot2 immundata patchwork

Imports (34)

dplyr dtplyr data.table cli pheatmap reshape2 circlize airr Rcpp magrittrmethodsscales rlang plyr stringdist readr stringr tibble tidyselect tidyr ape doParallel rlistutilsglue checkmate duckplyr dbplyr lifecycle purrrstatsvctrs ggthemes ggsci

LinkingTo (1)

Rcpp

Suggests (21)

knitr roxygen2 testthat pkgdown assertthat rmarkdown factoextra (>= 1.0.4)fpc ggpubr ggraph ggseqlogo igraph phangorn ggalluvial UpSetR ggrepel shiny shinythemes quarto MASS (>= 7.3)Rtsne

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Vadim I. Nazarov

Author, Maintainer

Authors (4)

Vadim I. Nazarov

Author, Maintainer

Ivan Balashov

Author · added in 0.6.7

Aleksandr A. Popov

Author · added in 0.6.7

Vasily O. Tsvetkov

Author

Listed in earlier versions (8)

ImmunoMind