recipe bioconductor-hdf5array

HDF5 backend for DelayedArray objects

Homepage

https://bioconductor.org/packages/3.12/bioc/html/HDF5Array.html

License

Artistic-2.0

Recipe

/bioconductor-hdf5array/meta.yaml

Links

biotools: hdf5array, doi: 10.1038/nmeth.3252

Implements the HDF5Array and TENxMatrix classes, 2 convenient and memory-efficient array-like containers for on-disk representation of HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. dense) HDF5 representation. TENxMatrix is for datasets that use the HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 Million Brain Cell Dataset). Both containers being DelayedArray extensions, they support all operations supported by DelayedArray objects. These operations can be either delayed or block-processed.

package bioconductor-hdf5array

Versions

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 >=0.36.0,<0.37.0

• bioconductor-delayedarray >=0.16.0,<0.17.0

• bioconductor-iranges >=2.24.0,<2.25.0

• bioconductor-rhdf5 >=2.34.0,<2.35.0

• bioconductor-rhdf5lib >=1.12.0,<1.13.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.5.0

• liblapack >=3.8.0,<4.0a0

• r-base >=4.0,<4.1.0a0

• r-matrix

Required By

• bioconductor-scmeth

• bioconductor-sesame

• bioconductor-curatedtcgadata

• bioconductor-glmgampoi

• bioconductor-minfi

• bioconductor-recountmethylation

• bioconductor-genomicscores

• bioconductor-mofa2

• bioconductor-dropletutils

• bioconductor-bsseq

• bioconductor-netsmooth

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

• bioconductor-hcadata

• bioconductor-delayedmatrixstats

• bioconductor-methylseqdata

• bioconductor-loomexperiment

• bioconductor-clusterexperiment

• bioconductor-genogam

• bioconductor-tenxbraindata

• bioconductor-signaturesearch

• bioconductor-tenxpbmcdata

• bioconductor-fraser

• bioconductor-methrix

• bioconductor-biscuiteer

• bioconductor-scry

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>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-hdf5array/README.html)