Bioconductor Zellkonverter

zellkonverter

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.22.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: cli, DelayedArray, Matrix, reticulate, S4Vectors, SingleCellExperiment, SparseArray, SummarizedExperiment
• Imports: basilisk, cli, DelayedArray, Matrix, reticulate, S4Vectors, SingleCellExperiment, SparseArray, SummarizedExperiment
• Install: BiocManager::install("zellkonverter")

When to Use

• Reading a SingleCellExperiment from a .h5ad file using readH5AD.
• Writing a SingleCellExperiment to a .h5ad file using writeH5AD.
• Converting directly between SingleCellExperiment and Python AnnData objects in memory using SCE2AnnData and AnnData2SCE.
• Setting up consistent Python environments for package developers using AnnDataDependencies.

When NOT to Use

• For converting Seurat objects directly to Python, use SeuratDisk or convert to SingleCellExperiment first, because zellkonverter strictly interfaces with SingleCellExperiment.
• For managing Python environments generally, use basilisk directly, as zellkonverter uses it internally but isn't a general-purpose environment manager.

Data Requirements

• A valid .h5ad file on disk for reading.
• A SingleCellExperiment object in R for writing or conversion.
• An AnnData object in Python (via reticulate) for in-memory conversion.

Key Parameters

• file: Path to the input .h5ad file in readH5AD or output destination in writeH5AD.
• verbose (FALSE): Logical indicating whether to display progress messages during conversion in readH5AD.
• version: String specifying the version of anndata to return dependencies for in AnnDataDependencies (e.g., "0.7.6").
• env: The basilisk environment to use, typically set to zellkonverterAnnDataEnv() in basiliskRun.

Best Practices

• Use basiliskRun with zellkonverterAnnDataEnv() to safely execute Python code on AnnData objects within a controlled environment.
• Use AnnDataDependencies() if you are a package developer to guarantee you are using the same versions of Python packages as zellkonverter.
• Turn on global progress messages using setZellkonverterVerbose(TRUE) if you want to monitor large conversions.

Common Pitfalls

• Python environment mismatches: Conversion failures due to missing or incompatible Python packages. Fix: Use basilisk to set up the Python environment before using SCE2AnnData or AnnData2SCE.
• Incompatible anndata versions: Custom environments failing to parse .h5ad files correctly. Fix: Check required versions with AnnDataDependencies() to ensure compatibility.
• Silent execution during long conversions: The process seems stalled when reading large .h5ad files. Fix: Set verbose = TRUE in readH5AD to display progress messages.

Alternatives

• basilisk: For general R/Python environment management without specific single-cell object conversion.
• reticulate: For direct Python interoperability in R, which zellkonverter wraps specifically for AnnData.
• scRNAseq: For accessing standard single-cell datasets natively in R without needing .h5ad files.

Citations

• Luke Zappia and Alan O'Callaghan (2021). "zellkonverter: Coercion Between Python AnnData and R SingleCellExperiment Objects." Journal of Open Source Software, 6(68), 3705.

References

• Homepage: https://bioconductor.org/packages/zellkonverter
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/zellkonverter/inst/doc/zellkonverter.html

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