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Installation Instructions for scRepertoire

Compiled: April 03, 2026

Source: vignettes/articles/Installation.Rmd
Installation.Rmd

GitHub (Development Branch)

scRepertoire is an active project with frequent updates based on user feedback. The most up-to-date version is available via GitHub and can be installed using devtools::install_github() or remotes::install_github().

immApex is a required dependency for the underlying processes of scRepertoire. Ensure both are called during installation if not using Bioconductor.

remotes::install_github(c("BorchLab/immApex", "BorchLab/scRepertoire@devel"))

Bioconductor (Stable Release)

The current stable version of scRepertoire is also available through Bioconductor. This will automatically install all dependencies including immApex.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scRepertoire")

Verifying Installation

After installation, confirm everything is working:

library(scRepertoire)

# Check version
packageVersion("scRepertoire")

# Quick test with built-in data
data("contig_list")
combined <- combineTCR(contig_list,
                       samples = c("P17B", "P17L", "P18B", "P18L",
                                   "P19B", "P19L", "P20B", "P20L"))

If this runs without errors, you are ready to go.

Troubleshooting

Bioconductor Version Mismatch

If you see errors about package versions being incompatible, ensure your Bioconductor installation is up to date:

BiocManager::install(version = "release")
BiocManager::valid()

Compilation Errors (Rcpp)

scRepertoire includes C++ code via Rcpp. If you encounter compilation errors:

  • macOS: Ensure Xcode command line tools are installed: xcode-select --install
  • Windows: Install Rtools
  • Linux: Ensure r-base-dev or equivalent is installed

Legacy Version 1

If you need the original version 1 of scRepertoire:

devtools::install_github("BorchLab/scRepertoire@v1")

Release Notes

A full copy of the changes in each version can be found in the NEWS/ChangeLog.

Next Steps