Package index • convert2anndata

Bidirectional conversion

Main entry points. Converters accept either an in-memory object or a path to an .h5ad / .rds file; cli_convert() is the command-line dispatcher that picks a direction from the file extension.

convert_anndata_to_seurat(): Convert an AnnData object (or a .h5ad file) to a Seurat object
convert_anndata_to_sce(): Convert an AnnData object (or a .h5ad file) to a SingleCellExperiment
convert_to_anndata(): Convert SingleCellExperiment to AnnData
convert_seurat_to_sce(): Convert Seurat or Other Object to SingleCellExperiment
cli_convert(): Command Line Interface for convert2anndata

Python environment

Helpers for wiring reticulate to a Python interpreter that has the anndata module installed, and for diagnosing misconfiguration.

setup_anndata_python(): Configure the Python interpreter used by reticulate for AnnData I/O
check_anndata_python(): Check that reticulate has a working Python with the `anndata` module
diagnose_anndata_python(): Print a diagnostic block for the currently-active Python env

AnnData component extractors

Lower-level accessors that pull individual pieces out of an AnnData object as R-native matrices / data frames. Useful when building a custom conversion.

extract_anndata_X(): Extract the primary count matrix from an AnnData object
extract_anndata_layers(): Extract layers from an AnnData object as a named list of matrices
extract_anndata_obsm(): Extract obsm embeddings from an AnnData object
extract_anndata_obsp(): Extract obsp (cell x cell) matrices from an AnnData object
extract_anndata_raw(): Extract `adata.raw` as a CsparseMatrix
anndata_names(): Extract obs/var names from an AnnData object

Attaching components to R objects

attach_reductions_seurat(): Attach obsm embeddings to a Seurat object as dimensional reductions
attach_alt_experiments_sce(): Attach altExps to SingleCellExperiment Object
convert_graph_to_colPair(): Convert Seurat Graph to colPair-Compatible Format

Internal building blocks

Exported for advanced use and testing, but not part of the recommended user-facing API. Most users only need the converters in the first section.

align_metadata_seurat(): Align Metadata to Cell Names in Seurat Object
convert_commands(): Convert SeuratCommand objects into a serializable format
create_combined_assay(): Create Combined Assay in Seurat Object
default_reduction_map(): Default mapping from AnnData obsm keys to Seurat reduction (name, key) pairs
ensure_csparse_matrix(): Ensure Sparse Matrix is in a Format Compatible with AnnData
extract_counts_matrix(): Extract Counts Matrix from Seurat Assay
extract_data(): Extract Data from SingleCellExperiment
extract_pairs(): Extract Pairwise Data from SingleCellExperiment
identify_alt_exps_seurat(): Identify Assays to Move to altExps in Seurat Object
preserve_reductions_seurat(): Preserve Dimensional Reductions from Seurat Object
process_alt_experiments(): Process Alternative Experiments
process_dimensional_reductions(): Process Dimensional Reductions
process_layers(): Process Layers in Seurat Assay
process_main_assay(): Process Main Assay
process_metadata_and_pairwise(): Process Metadata and Pairwise Matrices
process_other_assays(): Process Other Assays
timestamped_cat(): Print Messages with Timestamp
update_seurat_object(): Update Seurat Object if Necessary