Installation

This guide installs the analysis toolkit immunarch for repertoire analysis. The data layer immundata ships with immunarch and loads automatically, so you do not need to install it separately for typical workflows. Advanced users will find optional immundata install steps at the end.

Requirements

R ≥ 4.2 recommended
Internet access to install packages

1) Install `pak` (recommended installer)

R

install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))

2) Install `immunarch` (includes `immundata`)

Use the GitHub build if you want the newest features.

R

# Latest GitHub build
pak::pkg_install("immunomind/immunarch")

# Or install from CRAN when available
pak::pkg_install("immunarch")

Verify the installation

R

library(immunarch)
packageVersion("immunarch")
# immundata is bundled; it will be available when you load immunarch

Reproducible environments

Pin an exact version (tag or SHA) for papers and CI:

R

pak::pkg_install("immunomind/immunarch@v0.9.1")

Optional: install `immundata` alone

Only needed if you want to work directly with the data layer API, build ingestion pipelines, or contribute.

R

# Latest GitHub build
pak::pkg_install("immunomind/immundata")

# Or CRAN when available
pak::pkg_install("immundata")

# Pin a specific version
pak::pkg_install("immunomind/immundata@0.2.1")