Package index

Package Information

Overview and utilities

srtdisk-package srtdisk SeuratDisk

srtdisk: Extended HDF5-Based Single Cell File Format Support

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

SaveH5Seurat() as.h5Seurat()

Save a Seurat object to an h5Seurat file

LoadH5Seurat() 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

Connect()

Connect 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

SeuratToH5AD()

Direct Seurat to H5AD Conversion

LoadH5AD()

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

LoadH5MU()

Load a MuData H5MU file as a Seurat object

SaveH5MU() as.h5mu()

Save a Seurat object to an H5MU file

Loom Format

Loading and saving Loom files for interoperability with loompy

LoadLoom() as.Seurat(<loom>)

Load a Loom file as a Seurat object

SaveLoom() 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

Spatial Data Conversion

Converting spatial data between Seurat and AnnData formats

ConvertH5ADSpatialToSeurat()

Convert spatial coordinates from h5ad to Seurat format

ConvertSeuratSpatialToH5AD()

Convert Seurat spatial data to h5ad format

Format Conversion

General conversion utilities between all supported formats

Convert()

Convert single-cell datasets between formats

FileType()

Determine a filetype based on its extension

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

WriteAttribute()

Write an attribute to an HDF5 file, group, or 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

AppendData()

Append data from an h5Seurat file to a preexisting Seurat object

Transpose()

Transpose 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 an HDF5 compound dataset to a group

Writeable()

Is an HDF5 file or group writeable

WriteMode()

Get the proper HDF5 connection mode for writing depending on overwrite status