recipe bioconductor-gdsfmt

R Interface to CoreArray Genomic Data Structure (GDS) Files






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

(downloads) docker_bioconductor-gdsfmt



Required By


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

conda install bioconductor-gdsfmt

and update with:

conda update bioconductor-gdsfmt

or use the docker container:

docker pull<tag>

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