An R Package for quality assurance checking, normalization and batch effects adjustments of NanoString data suitable for single sample processing. This is the companion R package for the paper “Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction”, published in PLOS ONE.
You can install
nanostringr from CRAN with:
Or get the latest development version from GitHub:
# install.packages("devtools") devtools::install_github("TalhoukLab/nanostringr")
To see the full list of exported functions:
A quick overview of the key functions:
NanoStringQC: Computes quality assurance metrics.
HKnorm: Performs log (base 2) transformation and normalization to Housekeeping Genes
refMethod: Performs batch effect correction using the reference-based strategy
parse_counts: Read RCC files and extract raw counts data
parse_attributes: Read RCC files and extract expression annotation data
citation("nanostringr") for information on how to cite the PLOS ONE paper when using this package in publications.