recipe bioconductor-hdf5array

HDF5 backend for DelayedArray objects

Homepage

https://bioconductor.org/packages/3.13/bioc/html/HDF5Array.html

License

Artistic-2.0

Recipe

/bioconductor-hdf5array/meta.yaml

Links

biotools: hdf5array, doi: 10.1038/nmeth.3252

Implement 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.

package bioconductor-hdf5array

Versions

1.20.0-0,  1.18.1-0,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.1-0,  1.10.1-0,  1.8.1-0,  1.6.0-0

Depends

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-delayedarray >=0.18.0,<0.19.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-rhdf5 >=2.36.0,<2.37.0

• bioconductor-rhdf5filters >=1.4.0,<1.5.0

• bioconductor-rhdf5lib >=1.14.0,<1.15.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• liblapack >=3.8.0,<4.0a0

• r-base >=4.1,<4.2.0a0

• r-matrix

Required By

• bioconductor-biscuiteer

• bioconductor-genogam

• bioconductor-genomicscores

• bioconductor-spatialheatmap

• bioconductor-bsseq

• bioconductor-scry

• bioconductor-curatedtcgadata

• bioconductor-hcadata

• bioconductor-methylseqdata

• bioconductor-scmeth

• bioconductor-compartmap

• bioconductor-glmgampoi

• bioconductor-signaturesearch

• bioconductor-fraser

• bioconductor-clusterexperiment

• bioconductor-tenxpbmcdata

• bioconductor-methrix

• bioconductor-cytomapper

• bioconductor-imcdatasets

• bioconductor-gsva

• bioconductor-recountmethylation

• bioconductor-mafh5.gnomad.v3.1.1.grch38

• bioconductor-tenxbraindata

• bioconductor-loomexperiment

• bioconductor-mafh5.gnomad.r3.0.grch38

• bioconductor-mofa2

• bioconductor-minfi

• bioconductor-netsmooth

• bioconductor-dropletutils

• bioconductor-singlecellmultimodal

• bioconductor-magar

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-hdf5array

and update with:

conda update bioconductor-hdf5array

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-hdf5array:<tag>

(see bioconductor-hdf5array/tags for valid values for <tag>)

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