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:
install.packages("nanostringr")
Or get the latest development version from GitHub:
# install.packages("devtools")
# devtools::install_github("TalhoukLab/nanostringr")
install.packages("nanostringr", repos = c('https://talhouklab.r-universe.dev', 'https://cloud.r-project.org'))
To see the full list of exported functions:
library(nanostringr)
ls("package:nanostringr")
A quick overview of the key functions:
NanoStringQC: Computes quality assurance metrics.HKnorm: Performs log (base 2) transformation and normalization to Housekeeping GenesrefMethod: Performs batch effect correction using the reference-based strategyparse_counts: Read RCC files and extract raw counts dataparse_attributes: Read RCC files and extract expression annotation dataPlease see citation("nanostringr") for information on how to cite the PLOS ONE paper when using this package in publications.