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R Setup (optional)

R is an optional dependency required only for:

  • Differential expression — pseudobulk_edger, pseudobulk_limma
  • Imputation — ALRA

All other SCLab features work without R.

Step 1 — Install R

Download and install R (≥ 4.2) from https://cran.r-project.org.

Verify the installation:

R --version

Step 2 — Install R packages

Open an R console and run:

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

# For differential expression
BiocManager::install(c("edgeR", "limma", "MAST", "SingleCellExperiment"))

# For imputation (ALRA)
BiocManager::install("ALRA")

Step 3 — Install Python R bridge

pip install rpy2 anndata2ri

Or with uv:

uv add rpy2 anndata2ri

Step 4 — Verify

from sclab.tools.differential_expression import edger_is_available, limma_is_available

print("edgeR available:", edger_is_available())
print("limma available:", limma_is_available())

Troubleshooting

rpy2 cannot find R

Make sure R is on your PATH. You can set the R_HOME environment variable explicitly:

export R_HOME=$(R RHOME)

Package not found in R

Re-run the BiocManager install commands inside the same R version that rpy2 is pointing to.