seandavi/OmicIDXR: Query the OmicIDX genomic data index API

This R package accesses the OmicIDX project. OmicIDX parses and then serves public genomics repository metadata. These metadata are growing quickly, updated often, and are now very large when taken as a whole. Because of the interrelated nature of the metadata and the myriad approaches and use cases that exist, including search, bulk download, and even data mining, we serve the data via a GraphQL endpoint. Currently, OmicIDX contains the SRA and Biosample metadata sets. These overlap with each other, but SRA metadata contains deeper metadata than Biosample data on the same samples. Biosample, on the other hand, contains many more samples and currently includes metadata about a subset of NCBI GEO, all SRA samples, and some additional samples from projects like Genbank.

install.packages("remotes")
remotes::install_github("seandavi/OmicIDXR")