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nanostringr (version 0.6.0)

Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

Description

Provides quality control (QC), normalization, and batch effect correction operations for 'NanoString nCounter' data, Talhouk et al. (2016) . Various metrics are used to determine which samples passed or failed QC. Gene expression should first be normalized to housekeeping genes, before a reference-based approach is used to adjust for batch effects. Raw NanoString data can be imported in the form of Reporter Code Count (RCC) files.

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Install

install.packages('nanostringr')

Monthly Downloads

641

Version

0.6.0

License

MIT + file LICENSE

Issues

1

Pull Requests

0

Stars

5

Forks

3

Maintainer

Derek Chiu

Last Published

April 25th, 2025

Functions in nanostringr (0.6.0)

NanoStringQC

QC metrics for NanoString Data
expQC

Expression QC data
normalize_pools

Normalize data using common pools
cohort

NanoString Experiment Cohorts
rcc

Read NanoString RCC files
HKnorm

Normalization to Housekeeping Genes
normalize_random

Normalize data using random reference samples
CCplot

Concordance Correlation Plot
nanostringr-package

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

Reference-based approach for batch adjustment