Package: nanostringr 0.4.2

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

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:

4.48 score 5 stars 12 scripts 727 downloads 9 exports 29 dependencies

Last updated 5 months agofrom:5679542908. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	OK	Nov 19 2024
R-4.5-linux	OK	Nov 19 2024
R-4.4-win	OK	Nov 19 2024
R-4.4-mac	OK	Nov 19 2024
R-4.3-win	OK	Nov 19 2024
R-4.3-mac	OK	Nov 19 2024

Exports:CCplot HKnorm NanoStringQC normalize_pools normalize_random parse_attributes parse_counts read_rcc refMethod

Dependencies:assertthat ccaPP cli cpp11 DEoptimR dplyr fansi generics glue lifecycle magrittr mvtnorm pcaPP pillar pkgconfig purrr R6 Rcpp RcppArmadillo rlang robustbase stringi stringr tibble tidyr tidyselect utf8 vctrs withr

nanostringr Package

Rendered fromOverview.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-05-24
Started: 2016-09-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Concordance Correlation Plot	CCplot
NanoString Experiment Cohorts	cohort hld.r hlo.r ovc.r ovd.r ovo.r
Expression QC data	expQC
Normalization to Housekeeping Genes	HKnorm
QC metrics for NanoString Data	NanoStringQC
Normalize data using common pools	normalize_pools
Normalize data using random reference samples	normalize_random
Read NanoString RCC files	parse_attributes parse_counts rcc read_rcc
Reference-based approach for batch adjustment	refMethod