Package index • scConvert

Package Information

Overview and utilities

scConvert-package scConvert: scConvert: Universal Single-Cell Format Conversion for R
scdisk-class scdisk: A disk-based object for single-cell analysis
IsSCDisk(): Does an R6 class inherit from scdisk
GetSCDisk() RegisterSCDisk(): Get and Register scdisk Subclasses

h5Seurat Format

Working with h5Seurat files - the native HDF5-based R/Seurat format

writeH5Seurat() as.h5Seurat(): Save a Seurat object to an h5Seurat file
readH5Seurat() as.Seurat(<h5Seurat>): Load a Seurat object from an h5Seurat file
h5Seurat-class h5Seurat: A class for connections to h5Seurat files
Cells(<h5Seurat>) DefaultAssay(<h5Seurat>) `DefaultAssay<-`(<h5Seurat>) Idents(<h5Seurat>) IsGlobal(<H5Group>) Key(<H5Group>) Project(<h5Seurat>) `Project<-`(<h5Seurat>) Stdev(<h5Seurat>): Seurat bindings for h5Seurat files
scConnect(): scConnect to a single-cell HDF5 dataset
DefaultAssay(<h5SI>) print(<h5SI>): Tools for handling h5Seurat indexes

AnnData (h5ad) Format

Converting between Seurat and Python AnnData format

H5ADToH5Seurat(): Convert AnnData/H5AD files to h5Seurat files
H5SeuratToH5AD(): Convert h5Seurat files to H5AD files
writeH5AD(): Direct Seurat to H5AD Conversion
readH5AD(): Load an AnnData H5AD file as a Seurat object
readH5AD_obs(): Read observation metadata from an H5AD file
readH5AD_obsm(): Read observation embeddings from an H5AD file

MuData (h5mu) Format

Working with MuData multimodal HDF5 files

readH5MU(): Load a MuData H5MU file as a Seurat object
writeH5MU(): Write a Seurat object to h5mu format
as.h5mu(): Save a Seurat object to h5mu format
H5MUToH5Seurat(): Convert H5MU files to h5Seurat files
H5SeuratToH5MU(): Convert h5Seurat files to H5MU files
H5MUToH5AD(): Convert H5MU files to H5AD files (extract single modality)
H5ADToH5MU(): Convert an h5ad file to h5mu format
H5MUToLoom(): Convert an h5mu file to loom format
LoomToH5MU(): Convert a loom file to h5mu format
H5MUToZarr(): Convert an h5mu file to zarr format
ZarrToH5MU(): Convert a zarr store to h5mu format
H5MUToSOMA(): Convert H5MU (MuData) to SOMA format
SOMAToH5MU(): Convert SOMA to H5MU (MuData) format

Loom Format

Loading and saving Loom files for interoperability with loompy

readLoom() as.Seurat(<loom>): Load a Loom file as a Seurat object
writeLoom() as.loom(): Save a Seurat object to a Loom file
loom-class loom: A class for connections to loom files
DefaultAssay(<loom>) dim(<loom>): Seurat binding for loom files
LoadLoom0.1() LoadLoom3.0(): Loom-file Loading
LoomValidate0.1() LoomValidate3.0.0(): Validate Loom Files
LoomToH5Seurat(): Convert a loom file to h5seurat format
H5SeuratToLoom(): Convert an h5seurat file to loom format
LoomToH5AD(): Convert a loom file to h5ad format
H5ADToLoom(): Convert an h5ad file to loom format
LoomToZarr(): Convert a loom file to zarr format
ZarrToLoom(): Convert a zarr store to loom format
LoomToSOMA(): Convert Loom to SOMA format
SOMAToLoom(): Convert SOMA to Loom format

Zarr Format

Loading, saving, and converting Zarr-based AnnData stores

readZarr(): Load an AnnData Zarr store as a Seurat object
writeZarr(): Save a Seurat object as an AnnData Zarr store
H5ADToZarr(): Convert an h5ad file to zarr format
ZarrToH5AD(): Convert a zarr store to h5ad format
H5SeuratToZarr(): Convert an h5seurat file to zarr (AnnData) format
ZarrToH5Seurat(): Convert a zarr (AnnData) store to h5seurat format
ZarrToSOMA(): Convert Zarr to SOMA format
SOMAToZarr(): Convert SOMA to Zarr format

TileDB-SOMA Format

Reading and writing TileDB-SOMA for CELLxGENE Census interoperability

readSOMA(): Read a TileDB-SOMA experiment as a Seurat object
writeSOMA(): Write a Seurat object to TileDB-SOMA format
H5ADToSOMA(): Convert h5ad to SOMA format
SOMAToH5AD(): Convert SOMA to h5ad format
H5SeuratToSOMA(): Convert h5Seurat to SOMA format
SOMAToH5Seurat(): Convert SOMA to h5Seurat format

Spatial Data Conversion

Converting spatial data between Seurat, AnnData, and SpatialData formats

H5ADSpatialToSeurat(): Convert spatial coordinates from h5ad to Seurat format
SeuratSpatialToH5AD(): Convert Seurat spatial data to h5ad format
readSpatialData(): Read a SpatialData zarr store into a Seurat object
writeSpatialData(): Write a Seurat object to SpatialData zarr format
SpatialDataToH5AD(): Convert a SpatialData zarr store to h5ad format
H5ADToSpatialData(): Convert an h5ad file to SpatialData zarr format
SpatialDataToH5Seurat(): Convert a SpatialData zarr store to h5Seurat format
H5SeuratToSpatialData(): Convert an h5Seurat file to SpatialData zarr format
SpatialDataToZarr(): Convert a SpatialData zarr store to a standard anndata zarr store
ZarrToSpatialData(): Wrap a standard anndata zarr store as a SpatialData store

Format Conversion

General conversion utilities between all supported formats

scConvert(): Convert single-cell datasets between formats
FileType(): Convert an HDF5 compound dataset to a group (legacy version)
scConvert_cli(): Run the scconvert CLI for file-to-file conversion

Reading & Writing

Low-level HDF5 reading and writing functions

as.array(<H5D>) as.data.frame(<H5D>) as.data.frame(<H5Group>) as.list(<H5D>) as.list(<H5Group>) as.matrix(<H5D>) as.matrix(<H5Group>): Read HDF5 Files
as.sparse(<H5D>) as.sparse(<H5Group>): Convert an HDF5 dataset to a sparse matrix
WriteH5Group(): Write data to an HDF5 group
BasicWrite(): Write lists and other data to an HDF5 dataset
ImageWrite(): Write a SpatialImage object to an HDF5 dataset
SparseWrite(): Write a sparse matrix to an HDF5 dataset
AttrExists() Exists(): Check to see if a dataset, group, or attribute exists in an HDF5 file, group, or dataset
H5Path(): Create an HDF5 object path

Object Operations

Utilities for working with HDF5 objects and attributes

GetAssays() GetCommands() GetDimReducs() GetGraphs() GetImages() GetNeighbors(): Figure out which objects to load from an h5Seurat file
AssembleAssay() AssembleDimReduc() AssembleGraph() AssembleImage() AssembleNeighbor() AssembleSeuratCommand(): Assemble an object from an h5Seurat file
scAppendData(): Append data from an h5Seurat file to a preexisting Seurat object
scTranspose(): scTranspose a matrix
PadMatrix(): Pad a matrix

Testing & Validation

Functions for testing and validating HDF5 files and Seurat objects

IsDataFrame(<H5D>) IsDataFrame(<H5Group>) IsFactor(<H5D>) IsFactor(<H5Group>) IsList(<H5Group>) IsLogical(<H5D>) IsMatrix(<H5D>) IsMatrix(<H5Group>): Test HDF5 datasets and groups to see what kind of data they are
IsDataFrame() IsFactor() IsList() IsLogical() IsMatrix(): Test an object's class
CheckMatrix(): Check that a dataset is a proper loom matrix
IsMatrixEmpty(): Check to see if a matrix is empty

Data Type Utilities

Utilities for handling data types and format conversions

GuessDType(): Guess an HDF5 Datatype
IsDType(): Check the datatype of an HDF5 dataset
StringType(): Generate an HDF5 string dtype
BoolToInt(): Convert a logical to an integer
Dims(): Get the dimensions of an HDF5 dataset or sparse matrix
GetClass(): Get a class string with package information
GetMargin(): Determine the margin to use for a dataset
GetParent(): Get the parent of an HDF5 dataset or group
IndexToPointer() PointerToIndex(): Convert sparse matrix pointers to indices and vice versa
ClosestVersion(): Find the closest version
ChunkPoints(): Generate chunk points
MakeSpace(): Make a space

Metadata & Attributes

Working with HDF5 attributes and metadata

PadNames(): Add names for unnamed or partially named objects
RandomName(): Generate a random string of characters
FormatTime() Timestamp() TSFormats(): Create and work with timestamps
UpdateKey(): Update a Seurat key
UpdateSlots(): Update slots in an object
FixFeatures(): Fix Feature Names
CompoundToGroup(): Convert compound dataset to group
Writeable(): Is an HDF5 file or group writeable
WriteMode(): Get the proper HDF5 connection mode for writing depending on overwrite status

Internal

Internal functions and methods

AddAnndataEncoding(): Add AnnData encoding attributes to an HDF5 dataset or group
AddGenericSpatialData(): Add generic spatial data to Seurat object
AddSlideSeqSpatialData(): Add SlideSeq spatial data to Seurat object
AddVisiumSpatialData(): Add Visium spatial data to Seurat object
AnnDataLayerToSeurat(): Map AnnData layer name to Seurat layer name
AnnDataReductionKey(): Map AnnData reduction name to Seurat key
AssembleAssay() AssembleDimReduc() AssembleGraph() AssembleImage() AssembleNeighbor() AssembleSeuratCommand(): Assemble an object from an h5Seurat file
BasicWrite(): Write lists and other data to an HDF5 dataset
BoolToInt(): Convert a logical to an integer
CachedGuessDType(): Cached version of GuessDType for known string constants
CachedUtf8Type(): Get cached UTF-8 string dtype
CheckMatrix(): Check that a dataset is a proper loom matrix
ChunkPoints(): Generate chunk points
ClosestVersion(): Find the closest version
CompoundToGroup(): Convert compound dataset to group
ConvertBPCellsMatrix(): Convert BPCells matrix objects to dgCMatrix
ConvertFOVToH5AD(): Convert FOV object to h5ad-compatible structure
ConvertH5MUSpatialToSeurat(): Convert h5mu spatial data to Seurat format for a specific modality
CopyH5MatrixData(): Copy HDF5 matrix data handling nested paths
CreateCachedExistsChecker(): Create a cached HDF5 existence checker
DecodeCategorical(): Decode AnnData categorical encoding to R factor
DeconstructSparseCSR(): Deconstruct dgCMatrix to AnnData CSR components
DetectMultiLibrary(): Detect if h5Seurat file contains multi-library spatial data
DetectSpatialTechnology(): Detect spatial technology from data structure
Dims(): Get the dimensions of an HDF5 dataset or sparse matrix
DirectSeuratToH5AD(): Direct Seurat-to-h5ad write (single-pass, no intermediate h5Seurat)
EncodeCategorical(): Encode R factor as AnnData categorical
ExtractFOVCentroids(): Functions for handling FOV (Field of View) spatial objects
ExtractFOVMolecules(): Extract molecule positions from FOV object
ExtractFOVSegmentation(): Extract segmentation boundaries from FOV object
FileType(): Convert an HDF5 compound dataset to a group (legacy version)
FixFeatures(): Fix Feature Names
GetAssayDataCompat(): Get assay data with V4/V5 compatibility
GetAssayLayersCompat(): Get available layers or slots from assay
GetClass(): Get a class string with package information
GetCompressionLevel(): Get compression level for HDF5 dataset creation
GetDefaultAssayToModalityMapping(): Get default assay to modality name mapping
GetDefaultModalityMapping(): Get default modality to assay name mapping
GetFeaturesV5Safe(): Get feature names with V5 fallback
GetLayerPath(): Get Layer Path
GetMargin(): Determine the margin to use for a dataset
GetAssays() GetCommands() GetDimReducs() GetGraphs() GetImages() GetNeighbors(): Figure out which objects to load from an h5Seurat file
GetParent(): Get the parent of an HDF5 dataset or group
GetScaleFactors(): Get scale factors from Visium object
GetStringType(): Check if an HDF5 dataset is a factor
GuessDType(): Guess an HDF5 Datatype
H5ADToFOV(): Convert h5ad spatial data to FOV object
H5ADToH5Seurat(): Convert AnnData/H5AD files to h5Seurat files
AttrExists() Exists(): Check to see if a dataset, group, or attribute exists in an HDF5 file, group, or dataset
H5MUToH5AD(): Convert H5MU files to H5AD files (extract single modality)
H5MUToH5Seurat(): Convert H5MU files to h5Seurat files
H5Path(): Create an HDF5 object path
H5SeuratToH5AD(): Convert h5Seurat files to H5AD files
H5SeuratToH5MU(): Convert h5Seurat files to H5MU files
ImageWrite(): Write a SpatialImage object to an HDF5 dataset
IsAssay5(): Check if object is Assay5 (V5 format)
IsCompound(): Check for compound type in HDF5 dataset
IsDType(): Check the datatype of an HDF5 dataset
IsEffectively1D(): Check if H5D dataset is effectively 1D
IsMatrixEmpty(): Check to see if a matrix is empty
IsSCDisk(): Does an R6 class inherit from scdisk
IsV5Structure(): Check if h5Seurat file uses V5 structure
ListFormats(): List all registered format conversions
LoadLoom0.1() LoadLoom3.0(): Loom-file Loading
MakeSpace(): Make a space
MigrateV4ToV5(): Migrate V4 to V5 Structure
PB(): Create a progress bar
PadMatrix(): Pad a matrix
PadNames(): Add names for unnamed or partially named objects
PrepareSpatialForH5MU(): Prepare spatial data for h5mu export
RandomName(): Generate a random string of characters
ReadH5ImageDataset(): Read HDF5 image dataset with proper dimension handling
ReadLibraryIds(): Read library IDs from h5Seurat metadata
ReadSparseMatrix(): Read sparse matrix from HDF5
ReadV5Layer(): Read V5 Layer Data
ReconstructSparseCSR(): Reconstruct sparse CSR/CSC matrix from array components
RegisterDirectPath(): Register a direct conversion path between two file formats
RegisterFormat(): Register a file format with its load and save functions
RequiresS4Reconstruction(): Check if assay requires S4 slot reconstruction
ResolveNestedH5Path(): Resolve a nested HDF5 path to its object
RestoreSpatialFromH5MU(): Restore spatial data from h5mu file to Seurat object
SafeH5DRead(): Safely read an H5D dataset
SafeH5GroupToList(): Safely convert H5Group to list, handling 3D+ arrays
SafeSetLayerData(): Safely set layer data in a V5 Assay
SanitizeImageKey(): Sanitize string to valid Seurat image key
ScalarSpace(): Get cached scalar HDF5 dataspace
SetAssayDataCompat(): Set assay data with V4/V5 compatibility
SetFeaturesV5(): Set V5 feature index in HDF5 group
SeuratLayerToAnnData(): Map Seurat layer name to AnnData layer name
IndexToPointer() PointerToIndex(): Convert sparse matrix pointers to indices and vice versa
SparseWrite(): Write a sparse matrix to an HDF5 dataset
StringType(): Generate an HDF5 string dtype
IsDataFrame(<H5D>) IsDataFrame(<H5Group>) IsFactor(<H5D>) IsFactor(<H5Group>) IsList(<H5Group>) IsLogical(<H5D>) IsMatrix(<H5D>) IsMatrix(<H5Group>): Test HDF5 datasets and groups to see what kind of data they are
IsDataFrame() IsFactor() IsList() IsLogical() IsMatrix(): Test an object's class
FormatTime() Timestamp() TSFormats(): Create and work with timestamps
TransferMetadataV5(): Transfer metadata from V5 h5Seurat to h5ad
UpdateKey(): Update a Seurat key
UpdateSlots(): Update slots in an object
UtilsAssayCompat: Assay Compatibility Utility Functions
UtilsH5Access: HDF5 Access Utility Functions
V5LayerSupport: V5 Layer Support Functions
LoomValidate0.1() LoomValidate3.0.0(): Validate Loom Files
ValidateMultimodalObject(): Validate Seurat object for multimodal export
WriteH5SpatialV5(): Handle spatial data for V5 objects
WriteMode(): Get the proper HDF5 connection mode for writing depending on overwrite status
WriteV5Layer(): Write V5 Layer Data
Writeable(): Is an HDF5 file or group writeable
as.factor.H5D(): Convert an HDF5 dataset to a factor
.add_spatialdata_coords(): Add spatial coordinates from SpatialData to Seurat object
.assay_to_modality(): Map Seurat assay name to h5mu modality name
.attach_spatialdata_image(): Attach an image array to a Seurat object
.decode_vlen_utf8(): Decode vlen-utf8 encoded raw data to character vector
.encode_vlen_utf8(): Encode character vector to vlen-utf8 raw data
.h5ad_write_dict_group(): Write an AnnData dict-style empty group
.h5seurat_write_scaffold(): Write required h5seurat root attributes and empty groups
.modality_to_assay(): Map h5mu modality name to Seurat assay name
.ome_ngff_to_hwc(): Convert raw OME-NGFF array to height x width x channels format
.raw_to_r_type(): Convert raw bytes to R type
.read_ome_ngff_image(): Read an OME-NGFF image from a zarr directory
.read_spatialdata_points(): Read points from a SpatialData points directory
.read_spatialdata_shapes(): Read shapes from a SpatialData shapes directory
.sd_read_column(): Read a single column from a zarr DataFrame
.soma_has_write_soma(): Check whether tiledbsoma::write_soma is available
.soma_read_extra_measurements(): Read additional measurements as extra assays
.soma_read_obs(): Read obs from a SOMA experiment
.soma_read_obsm(): Read obsm embeddings from a SOMA measurement
.soma_read_obsp(): Read obsp graphs from a SOMA measurement
.soma_read_var(): Read var from a SOMA measurement
.soma_read_x(): Read X matrix from a SOMA measurement
.stream_composite_via_h5seurat(): Run two-step streaming conversion via a temp h5seurat file
.stream_dense_matrix(): Stream a dense matrix from one HDF5 file to another
.stream_h5ad_df_to_h5seurat_md(): Stream an h5ad-style DataFrame group to h5seurat meta.data
.stream_h5mu_to_h5seurat(): Stream h5mu to h5seurat (direct HDF5-to-HDF5)
.stream_h5seurat_md_to_h5ad_df(): Stream h5seurat meta.data to an h5ad-style DataFrame group
.stream_h5seurat_to_h5mu(): Stream h5seurat to h5mu (direct HDF5-to-HDF5)
.stream_h5seurat_to_loom(): Stream h5seurat to loom (direct HDF5-to-HDF5)
.stream_loom_to_h5seurat(): Stream loom to h5seurat (direct HDF5-to-HDF5)
.stream_sparse_group(): Stream a sparse matrix group from one HDF5 file to another
.write_ome_ngff_image(): Write an image as an OME-NGFF zarr store
.write_spatialdata_points(): Write point coordinates as a SpatialData points directory
.write_spatialdata_shapes(): Write spatial coordinates as a SpatialData shapes directory
.zarr_chunk_path_v2(): Build chunk file path for zarr v2
.zarr_compress(): Compress chunk data
.zarr_create_group(): Create a zarr v2 group directory with metadata
.zarr_decompress(): Decompress chunk data
.zarr_get_n_obs(): Get number of observations from zarr store
.zarr_get_n_vars(): Get number of variables from zarr store
.zarr_list_children(): List children of a zarr group
.zarr_node_type(): Determine zarr node type
.zarr_parallel_write(): Write multiple zarr arrays in parallel
.zarr_parse_dtype(): Parse zarr v2 dtype string to R type info
.zarr_read_anndata_column(): Read an AnnData DataFrame column from zarr store
.zarr_read_anndata_index(): Read AnnData index from obs or var group
.zarr_read_anndata_index_from_attrs(): Read an anndata index given pre-read attrs
.zarr_read_anndata_matrix(): Read an AnnData matrix (dense or sparse) from zarr store
.zarr_read_attrs(): Read zarr node attributes
.zarr_read_chunked(): Read multi-chunk zarr v2 numeric array
.zarr_read_json(): Read and parse a JSON file
.zarr_read_numeric(): Read a zarr v2 numeric array from disk
.zarr_read_strings(): Read a vlen-utf8 encoded string array from zarr v2 store
.zarr_store_version(): Detect zarr store format version
.zarr_write_anndata_dataframe(): Write an AnnData DataFrame (obs or var) to zarr store
.zarr_write_attrs(): Write zarr attributes to .zattrs file
.zarr_write_numeric(): Write a zarr v2 numeric array
.zarr_write_strings(): Write a zarr v2 vlen-utf8 string array
DefaultAssay(<h5SI>) print(<h5SI>): Tools for handling h5Seurat indexes
sc_find_cli(): Find the scconvert CLI binary