Package: rhdf5client 1.29.0

Vincent Carey

rhdf5client: Access HDF5 content from HDF Scalable Data Service

This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

Authors:Samuela Pollack [aut], Shweta Gopaulakrishnan [aut], BJ Stubbs [aut], Alexey Sergushichev [aut], Vincent Carey [cre, aut]

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rhdf5client.pdf |rhdf5client.html✨
rhdf5client/json (API)
NEWS

# Install 'rhdf5client' in R:
install.packages('rhdf5client', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:rhdf5client-1.29.0(bioc 3.21)rhdf5client-1.28.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dataimportsoftwareinfrastructure

4.82 score 2 packages 37 scripts 335 downloads 1 mentions 12 exports 24 dependencies

Last updated 4 months agofrom:65b8c5d8e8. Checks:4 OK, 7 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 13 2025
R-4.5-win-x86_64ERRORFeb 13 2025
R-4.5-mac-x86_64ERRORFeb 13 2025
R-4.5-mac-aarch64OKFeb 13 2025
R-4.5-linux-x86_64ERRORFeb 13 2025
R-4.4-win-x86_64ERRORFeb 13 2025
R-4.4-mac-x86_64ERRORFeb 13 2025
R-4.4-mac-aarch64OKFeb 13 2025
R-4.3-win-x86_64ERRORFeb 13 2025
R-4.3-mac-x86_64ERRORFeb 13 2025
R-4.3-mac-aarch64OKFeb 13 2025

Exports:check_hsdsextractCompoundJSONgetDataHSDSArrayHSDSDatasetHSDSFileHSDSSourceisplitlistDatasetslistDomainssprocURL_hsds

Dependencies:abindaskpassBiocGenericscrayoncurldata.tableDelayedArraygenericshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6rjsonS4ArraysS4VectorsSparseArraysysXVector

HSDSArray -- DelayedArray backend for Remote HDF5

Samuela Pollack and others

Rendered fromdelayed-array.Rmdusingknitr::rmarkdownon Feb 13 2025.

Last update: 2023-07-10
Started: 2018-10-02

Readme and manuals

Help Manual

Help pageTopics
bracket method for 1d request from HSDSDataset[,HSDSDataset,numeric,ANY,ANY-method
bracket method for 2d request from HSDSDataset[,HSDSDataset,numeric,numeric,ANY-method
Coercion method from HSDSMatrix to its superclass HSDSArrayas
a test requestcheck_hsds
Obtain dimensions of an object of type HSDSArraySeeddim dim,HSDSArraySeed-method
Obtain names of dimensions for an object of type HSDSArraySeeddimnames dimnames,HSDSArraySeed-method
Access dataset backed by an HSDSArraySeedextract_array extract_array,HSDSArraySeed-method
compound operationextractCompoundJSON
extract elements of a one or two-dimensional HSDSDatasetgetData getData,HSDSDataset,character,character-method getData,HSDSDataset,character,missing-method getData,HSDSDataset,list,,missing-method getData,HSDSDataset,list,character-method getData,HSDSDataset,list,missing-method
A DelayedArray backend for accessing a remote HDF5 server.HSDSArray HSDSArray-class
HSDSArraySeed for HSDSArray backend to DelayedArrayHSDSArraySeed HSDSArraySeed-class
Construct an object of type HSDSDataset A HSDSDataset is a representation of a dataset in a HDF5 file.HSDSDataset
An S4 class to represent a dataset in a HDF5 file.HSDSDataset-class
Construct an object of type HSDSFileHSDSFile
An S4 class to represent an HDF5 file accessible from a server.HSDSFile-class
DelayedMatrix subclass for a two-dimensional HSDSArrayHSDSMatrix HSDSMatrix-class
Construct an object of type HSDSSource.HSDSSource
An S4 class to represent a HDF5 server listening on a port.HSDSSource-class
This function is deprecated and will be defunct in the next release.isplit sproc
Search inner file hierarchy for datasetslistDatasets
List files and subdirectories of a domainlistDomains listDomains,HSDSSource,character-method listDomains,HSDSSource,missing-method
rhdf5client: A package for accessing HDFGroup HDF5 servers from R.rhdf5client
Deprecated functions in package 'rhdf5client'rhdf5client-deprecated
manage hsds URLURL_hsds