harmorust

Rust kernels for Harmony, with the same RunHarmony() API as the immunogenomics R package. Pair it with seurust: Seurat / seurust produce the PCA embedding, harmorust corrects it.

Install

Requires R ≥ 4.2 and, for source installs, a Rust toolchain (rustc + Cargo ≥ 1.89).

From r-universe

install.packages(
  "harmorust",
  repos = c("https://NebilI.r-universe.dev", "https://cloud.r-project.org")
)

From GitHub

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("NebilI/harmony-rs", subdir = "r/harmorust")

From a release tarball

install.packages("harmorust_0.1.0.tar.gz", repos = NULL, type = "source")

Source installs compile the harmorust CLI and put it in the package bin directory. Override with HARMORUST_BIN only if you want a different binary.

Example

library(harmorust)

# matrix form (cells × PCs) — same arguments as harmony::RunHarmony
corrected <- RunHarmony(
  pca_matrix, meta_data, vars_use = "donor",
  nclust = 20, return_object = TRUE
)
HarmonyConvergencePlot(corrected)

# Seurat / seurust workflow
# seurat <- RunPCA(seurat)
# seurat <- harmorust::RunHarmony(seurat, group.by.vars = "donor")

See the repository README for the Rust crate, parity notes, and publishing pipeline.