Package: HDF5Array 1.35.2

Hervé Pagès

HDF5Array: HDF5 datasets as array-like objects in R

The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.

Authors:Hervé Pagès

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HDF5Array/json (API)
NEWS

# Install 'HDF5Array' in R:
install.packages('HDF5Array', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioconductor/hdf5array/issues

Uses libs:
  • openssl– Secure Sockets Layer toolkit
  • curl– Easy-to-use client-side URL transfer library
  • zlib– Compression library

On BioConductor:HDF5Array-1.35.1(bioc 3.21)HDF5Array-1.34.0(bioc 3.20)

infrastructuredatarepresentationdataimportsequencingrnaseqcoverageannotationgenomeannotationsinglecellimmunooncologybioconductor-packagecore-packageopensslcurlzlib

12.10 score 11 stars 131 packages 804 scripts 27k downloads 3 mentions 80 exports 18 dependencies

Last updated 5 days agofrom:86705e10f3. Checks:OK: 1 NOTE: 3 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-win-x86_64WARNINGNov 30 2024
R-4.5-linux-x86_64NOTENov 30 2024
R-4.4-win-x86_64WARNINGNov 30 2024
R-4.4-mac-x86_64WARNINGNov 30 2024
R-4.4-mac-aarch64WARNINGNov 30 2024
R-4.3-win-x86_64WARNINGNov 30 2024
R-4.3-mac-x86_64NOTENov 30 2024
R-4.3-mac-aarch64NOTENov 30 2024

Exports:appendDatasetCreationToHDF5DumpLogcheck_and_delete_fileschunkdimcloseclose.H5Fileclose.H5FileIDcoercecreate_dirDelayedArraydestroy_H5DSetDescriptorextract_arrayextract_sparse_arrayextractNonzeroDataByColextractNonzeroDataByRowget_h5dimnamesget_h5mread_returned_typegetHDF5DumpChunkDimgetHDF5DumpChunkLengthgetHDF5DumpChunkShapegetHDF5DumpCompressionLevelgetHDF5DumpDirgetHDF5DumpFilegetHDF5DumpNameH5ADMatrixH5ADMatrixSeedH5DSetDescriptorH5FileH5FileIDh5lsh5mreadh5mread_from_reshapedh5readDimnamesH5SparseMatrixH5SparseMatrixSeedh5writeDimnamesHDF5ArrayHDF5ArraySeedHDF5RealizationSinkis_sparseis_sparse<-loadHDF5SummarizedExperimentlsHDF5DumpFilematrixClassnzcountopen.H5Fileopen.H5FileIDpathpath<-quickResaveHDF5SummarizedExperimentreplace_dirReshapedHDF5ArrayReshapedHDF5ArraySeedrestore_absolute_assay2h5_linkssaveHDF5SummarizedExperimentset_h5dimnamessetHDF5DumpChunkLengthsetHDF5DumpChunkShapesetHDF5DumpCompressionLevelsetHDF5DumpDirsetHDF5DumpFilesetHDF5DumpNameshorten_assay2h5_linksshowshowHDF5DumpLogstop_if_bad_dirtt.CSC_H5ADMatrixSeedt.CSC_H5SparseMatrixSeedt.CSR_H5ADMatrixSeedt.CSR_H5SparseMatrixSeedTENxMatrixTENxMatrixSeedTENxRealizationSinktypeupdateObjectvalidate_HDF5ArraySeed_dataset_geometrywrite_blockwrite_h5_assayswriteHDF5ArraywriteTENxMatrix

Dependencies:abindBiocGenericscrayonDelayedArraygenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsrhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsSparseArrayXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objectsclass:H5ADMatrix DelayedArray,H5ADMatrixSeed-method extractNonzeroDataByCol,H5ADMatrix-method extractNonzeroDataByRow,H5ADMatrix-method H5ADMatrix H5ADMatrix-class nzcount,H5ADMatrix-method
H5ADMatrixSeed objectsclass:CSC_H5ADMatrixSeed class:CSR_H5ADMatrixSeed class:Dense_H5ADMatrixSeed class:H5ADMatrixSeed CSC_H5ADMatrixSeed CSC_H5ADMatrixSeed-class CSR_H5ADMatrixSeed CSR_H5ADMatrixSeed-class Dense_H5ADMatrixSeed Dense_H5ADMatrixSeed-class dimnames,Dense_H5ADMatrixSeed-method H5ADMatrixSeed H5ADMatrixSeed-class t,CSC_H5ADMatrixSeed-method t,CSR_H5ADMatrixSeed-method t.CSC_H5ADMatrixSeed t.CSR_H5ADMatrixSeed
H5File objectscharacter_OR_H5File character_OR_H5File-class class:character_OR_H5File class:H5DSetDescriptor class:H5File class:H5FileID close.H5File close.H5FileID coerce,H5File,H5IdComponent-method destroy_H5DSetDescriptor H5DSetDescriptor H5DSetDescriptor-class H5File H5File-class H5FileID H5FileID-class open.H5File open.H5FileID path,H5File-method show,H5DSetDescriptor-method show,H5File-method show,H5FileID-method
A wrapper to rhdf5::h5ls() that works on H5File objectsh5ls
An alternative to 'rhdf5::h5read'get_h5mread_returned_type h5mread
Read data from a virtually reshaped HDF5 dataseth5mread_from_reshaped
HDF5 sparse matrices as DelayedMatrix objectsclass:H5SparseMatrix DelayedArray,H5SparseMatrixSeed-method extractNonzeroDataByCol,H5SparseMatrix-method extractNonzeroDataByRow,H5SparseMatrix-method H5SparseMatrix H5SparseMatrix-class nzcount,H5SparseMatrix-method
H5SparseMatrixSeed objectschunkdim,CSC_H5SparseMatrixSeed-method chunkdim,CSR_H5SparseMatrixSeed-method class:CSC_H5SparseMatrixSeed class:CSR_H5SparseMatrixSeed class:H5SparseMatrixSeed CSC_H5SparseMatrixSeed CSC_H5SparseMatrixSeed-class CSR_H5SparseMatrixSeed CSR_H5SparseMatrixSeed-class dim,H5SparseMatrixSeed-method dimnames,H5SparseMatrixSeed-method extractNonzeroDataByCol extractNonzeroDataByCol,CSC_H5SparseMatrixSeed-method extractNonzeroDataByRow extractNonzeroDataByRow,CSR_H5SparseMatrixSeed-method extract_array,H5SparseMatrixSeed-method extract_sparse_array,CSC_H5SparseMatrixSeed-method extract_sparse_array,CSR_H5SparseMatrixSeed-method H5SparseMatrixSeed H5SparseMatrixSeed-class is_sparse,H5SparseMatrixSeed-method nzcount,H5SparseMatrixSeed-method path,H5SparseMatrixSeed-method path<-,H5SparseMatrixSeed-method show,H5SparseMatrixSeed-method t,CSC_H5SparseMatrixSeed-method t,CSR_H5SparseMatrixSeed-method t.CSC_H5SparseMatrixSeed t.CSR_H5SparseMatrixSeed
Write/read the dimnames of an HDF5 datasetget_h5dimnames h5readDimnames h5writeDimnames set_h5dimnames
HDF5 dump managementappendDatasetCreationToHDF5DumpLog dump-management getHDF5DumpChunkDim getHDF5DumpChunkLength getHDF5DumpChunkShape getHDF5DumpCompressionLevel getHDF5DumpDir getHDF5DumpFile getHDF5DumpName HDF5-dump-management lsHDF5DumpFile setHDF5DumpChunkLength setHDF5DumpChunkShape setHDF5DumpCompressionLevel setHDF5DumpDir setHDF5DumpFile setHDF5DumpName showHDF5DumpLog
HDF5 datasets as DelayedArray objectsclass:HDF5Array class:HDF5Matrix coerce,ANY,HDF5Matrix-method coerce,HDF5Array,HDF5Matrix-method coerce,HDF5Matrix,HDF5Array-method DelayedArray,HDF5ArraySeed-method HDF5Array HDF5Array-class HDF5Matrix HDF5Matrix-class is_sparse<-,HDF5Array-method matrixClass,HDF5Array-method
HDF5ArraySeed objectschunkdim,HDF5ArraySeed-method class:HDF5ArraySeed dim,HDF5ArraySeed-method dimnames,HDF5ArraySeed-method extract_array,HDF5ArraySeed-method extract_sparse_array,HDF5ArraySeed-method HDF5ArraySeed HDF5ArraySeed-class is_sparse,HDF5ArraySeed-method is_sparse<-,HDF5ArraySeed-method path,HDF5ArraySeed-method path<-,HDF5ArraySeed-method type,HDF5ArraySeed-method updateObject,HDF5ArraySeed-method
Virtually reshaped HDF5 datasets as DelayedArray objectsclass:ReshapedHDF5Array class:ReshapedHDF5Matrix coerce,ANY,ReshapedHDF5Matrix-method coerce,ReshapedHDF5Array,ReshapedHDF5Matrix-method coerce,ReshapedHDF5Matrix,ReshapedHDF5Array-method DelayedArray,ReshapedHDF5ArraySeed-method matrixClass,ReshapedHDF5Array-method ReshapedHDF5Array ReshapedHDF5Array-class ReshapedHDF5Matrix ReshapedHDF5Matrix-class
ReshapedHDF5ArraySeed objectschunkdim,ReshapedHDF5ArraySeed-method class:ReshapedHDF5ArraySeed dim,ReshapedHDF5ArraySeed-method extract_array,ReshapedHDF5ArraySeed-method ReshapedHDF5ArraySeed ReshapedHDF5ArraySeed-class
Save/load an HDF5-based SummarizedExperiment objectloadHDF5SummarizedExperiment quickResaveHDF5SummarizedExperiment saveHDF5SummarizedExperiment
10x Genomics datasets as DelayedMatrix objectsclass:TENxMatrix DelayedArray,TENxMatrixSeed-method extractNonzeroDataByCol,TENxMatrix-method nzcount,TENxMatrix-method TENxMatrix TENxMatrix-class
TENxMatrixSeed objectsclass:TENxMatrixSeed TENxMatrixSeed TENxMatrixSeed-class
Write an array-like object to an HDF5 filechunkdim,HDF5RealizationSink-method class:HDF5RealizationSink coerce,ANY,HDF5Array-method coerce,DelayedArray,HDF5Array-method coerce,DelayedMatrix,HDF5Matrix-method coerce,HDF5RealizationSink,DelayedArray-method coerce,HDF5RealizationSink,HDF5Array-method coerce,HDF5RealizationSink,HDF5ArraySeed-method dimnames,HDF5RealizationSink-method HDF5RealizationSink HDF5RealizationSink-class is_sparse,HDF5RealizationSink-method type,HDF5RealizationSink-method writeHDF5Array write_block,HDF5RealizationSink-method
Write a matrix-like object as an HDF5-based sparse matrixchunkdim,TENxRealizationSink-method class:TENxRealizationSink close,TENxRealizationSink-method coerce,ANY,TENxMatrix-method coerce,DelayedArray,TENxMatrix-method coerce,DelayedMatrix,TENxMatrix-method coerce,TENxRealizationSink,DelayedArray-method coerce,TENxRealizationSink,TENxMatrix-method coerce,TENxRealizationSink,TENxMatrixSeed-method dimnames,TENxRealizationSink-method TENxRealizationSink TENxRealizationSink-class type,TENxRealizationSink-method writeTENxMatrix write_block,TENxRealizationSink-method