| name | bioconductor-zellkonverter |
| description | Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes f |
| when_to_use | Use when: 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.. Not for: 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 zel |
| user-invocable | false |
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
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