Nanostringbionet: Integrated R Framework For Bioscience Knowledge Discovery From Nanostring Ncounter Data

The NanoString nCounter Analysis System is a medium-throughput gene expression quantification technique that is becoming increasingly popular in the fields of immunology and oncology due to its ease of use and sensitivity, particularly in the analysis of formalin-fixed paraffin embedded samples. Despite the growing interest in NanoString, systematic analysis frameworks for the reproducible analysis of nCounter data remain limited. NanoStringBioNet is a pair of R packages that form a semi-automatic, open source framework for integrative and systematic knowledge discovery from nCounter datasets. Using the NSData module, NanoStringBioNet preprocesses a raw NanoString dataset and stores it in Biobase format for sharability. Subsequently, the NSFunc module performs downstream analyses such as enrichment and network inference of stable differentially expressed gene clusters by leveraging existing data analysis tools and custom script.