How do I install scib with R dependencies?

Use pip with extras, e.g., 'pip install scib[rpy2]', and separately install R packages like kBET via R commands as specified in the README. This ensures compatibility but adds setup complexity.

What's the difference between scib and scanpy for integration?

scib extends scanpy by providing standardized metrics and workflows specifically for benchmarking integration methods, whereas scanpy is a general toolkit for single-cell analysis without built-in evaluation suites.

How to benchmark a new integration method with scib?

Use the scib.metrics module to evaluate your method's output against the standard metrics, and integrate it into the scib-pipeline for automated comparisons with existing tools, following the documentation.

Does scib work with Seurat?

Yes, scib supports Seurat v3 integration, but it requires optional dependencies and might involve data conversion between Python and R, which can be tricky for seamless workflows.

scib or Harmony for integration evaluation?

scib is a benchmarking framework that can evaluate Harmony among other methods; it's not a direct alternative—use scib to assess Harmony's performance against metrics like Batch ASW in your datasets.

scIB (Single-cell Integration Benchmarks) — Single-Cell Genomics Integration Benchmarks

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scIB (Single-cell Integration Benchmarks) — Single-Cell Genomics Integration Benchmarks | Open Awesome

scIB (Single-cell Integration Benchmarks)

What is scIB (Single-cell Integration Benchmarks)?

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