bioconductor-gdsfmt

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This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are 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.

Home http://bioconductor.org/packages/3.7/bioc/html/gdsfmt.html
Versions 1.16.0, 1.14.1
License LGPL-3
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-gdsfmt

Installation

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

conda install bioconductor-gdsfmt

and update with:

conda update bioconductor-gdsfmt

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-gdsfmt.