Package: nanostringr 0.5.0

Derek Chiu

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

Provides quality control (QC), normalization, and batch effect correction operations for 'NanoString nCounter' data, Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. 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.

Authors:Derek Chiu [aut, cre], Aline Talhouk [aut], Samuel Leung [aut]

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nanostringr.pdf |nanostringr.html✨
nanostringr/json (API)
NEWS

# Install 'nanostringr' in R:
install.packages('nanostringr', repos = c('https://talhouklab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/talhouklab/nanostringr/issues

Pkgdown site:https://talhouklab.github.io

Datasets:
  • expQC - Expression QC data
  • hld.r - NanoString Experiment Cohorts
  • hlo.r - NanoString Experiment Cohorts
  • ovc.r - NanoString Experiment Cohorts
  • ovd.r - NanoString Experiment Cohorts
  • ovo.r - NanoString Experiment Cohorts

On CRAN:

Conda:

4.95 score 5 stars 12 scripts 694 downloads 9 exports 29 dependencies

Last updated 2 months agofrom:261ac46440. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 07 2025
R-4.5-winOKMar 07 2025
R-4.5-macOKMar 07 2025
R-4.5-linuxOKMar 07 2025
R-4.4-winOKMar 07 2025
R-4.4-macOKMar 07 2025
R-4.4-linuxOKMar 07 2025
R-4.3-winOKMar 07 2025
R-4.3-macOKMar 07 2025

Exports:CCplotHKnormNanoStringQCnormalize_poolsnormalize_randomparse_attributesparse_countsread_rccrefMethod

Dependencies:assertthatccaPPclicpp11DEoptimRdplyrfansigenericsgluelifecyclemagrittrmvtnormpcaPPpillarpkgconfigpurrrR6RcppRcppArmadillorlangrobustbasestringistringrtibbletidyrtidyselectutf8vctrswithr

nanostringr Package

Rendered fromOverview.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-02-01
Started: 2016-09-08