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NanoString QC, normalization, batch effect correction
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nanostringr.Rproj

README.md

nanostringr

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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("OVCARE/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.

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