README.md

In AlineTalhouk/nanostringr: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

nanostringr

Overview

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.

Installation

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")

Usage

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 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

Please see citation("nanostringr") for information on how to cite the PLOS ONE paper when using this package in publications.

AlineTalhouk/nanostringr documentation built on Aug. 26, 2023, 4:55 a.m.