nanostringr

0.6.1

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

0packages depend

7.8Kdownloads / year

74.2%test coverage

13/13checks pass

Overview

About

Maintained by Derek ChiuFirst published 2019-03-1513 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("nanostringr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("TalhoukLab/nanostringr")

Development version from TalhoukLab/nanostringr. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-nanostringr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-nanostringr

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-nanostringr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.21

74.2%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-08
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

7.8K

CRAN downloads in the past year

Rank #5,480 · ~21/day · ~650/mo

Releases R versions

Daily download trend is not available in this view yet.

39830 days

1.6K90 days

7.8K1 year

Compare downloads with other packages →

Also on94 r2u30 autocran2.1K conda_forge15 c2d4u

Repository

GitHub ↗ talhouklab/nanostringr

6Stars

3Forks

2Open issues

0Open PRs

13Releases

343Commits

3Contributors

343 commits · Last activity 2025-06-20 · 0% stars, 30d

Stars over time

2024-06-24 · 52026-07-07 · 6

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/talhouklab/nanostringr on 2026-07-30.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2

Imports (7)

assertthat ccaPP dplyr purrr rlang tibble tidyr

LinkingTo (0)

none

Suggests (4)

covr knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Derek Chiu

Author, Maintainer

Authors (3)

Derek Chiu

Author, Maintainer

Samuel Leung

Author

Aline Talhouk

Author

Package Timeline

13 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.6.1Latest
2025-05-05 · current release · diff ↗
0.6.0
2025-04-26 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.5.0
2025-02-05 · diff ↗
0.4.2
2024-06-11 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.4.1
2023-08-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.4.0
2022-08-20 · diff ↗
0.3.0
2022-05-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.2.0
2021-02-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.4
2019-05-09 · diff ↗

Show 6 earlier events

R
R 3.6.0 released · 2019-04-26
0.1.3
2019-04-24 · diff ↗
0.1.2
2019-04-03 · diff ↗
0.1.1
2019-03-25 · diff ↗
0.1.0
2019-03-15
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-15
Total releases: 13 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.2
Bundled data: 135 KB / 6 files
Download size: 507 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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