recipe bioconductor-gdsfmt

R Interface to CoreArray Genomic Data Structure (GDS) Files

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/gdsfmt.html

License:

LGPL-3

Recipe:

/bioconductor-gdsfmt/meta.yaml

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

package bioconductor-gdsfmt

Versions:

1.34.0-1,  1.34.0-0,  1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.1-0,  1.26.0-0,  1.24.0-0, 

1.34.0-1,  1.34.0-0,  1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.1-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.1-0,  1.16.0-0,  1.14.1-0

Depends:

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

Required By:

• bioconductor-saigegds

• bioconductor-seqsqc

• bioconductor-ggmanh

• bioconductor-seqarray

• bioconductor-genesis

• bioconductor-seqvartools

• bioconductor-variantexperiment

• bioconductor-scarray

• bioconductor-snprelate

• bioconductor-bigmelon

• bioconductor-gdsarray

• bioconductor-gbscleanr

• bioconductor-cnvranger

• bioconductor-gwastools

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-gdsfmt

and update with:

conda update bioconductor-gdsfmt

or use the docker container:

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

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

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