NACHO

2.0.6

NanoString Quality Control Dashboard

0packages depend

3.8Kdownloads / year

97.6%test coverage

13/13checks pass

Overview

About

Maintained by Mickaël CanouilFirst published 2019-04-2814 releasesCRAN page ↗GitHub ↗

NanoString nCounter data are gene expression assays where there is no need for the use of enzymes or amplification protocols and work with fluorescent barcodes (Geiss et al. (2018) doi:10.1038/nbt1385). Each barcode is assigned a messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its target can be counted. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString quality Control dasHbOard) is able to analyse the exported NanoString nCounter data and facilitates the user in performing a quality control. 'NACHO' does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application.

Install

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

install.packages("NACHO", 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("mcanouil/NACHO")

Development version from mcanouil/NACHO. 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-nacho

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-NACHO

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-NACHO

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

Health

CRAN checks

13OK

Slowest check: 5.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 6.11

97.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 417 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 57%
References docs: 0%

Downloads

3.8K

CRAN downloads in the past year

Rank #12,124 · ~10/day · ~314/mo

Releases R versions

Daily download trend is not available in this view yet.

29430 days

84690 days

3.8K1 year

Compare downloads with other packages →

Also on106 r2u1 autocran2.7K conda_forge31 c2d4u

Repository

GitHub ↗ mcanouil/nacho

9Stars

4Forks

0Open issues

0Open PRs

29Releases

743Commits

5Contributors

nanostringshinyquality-controlnormalisationr-packager-statsrstatsmirna

License GPL-3.0 · 743 commits · Last activity 2024-01-12 · 0% stars, 30d

Stars over time

2024-09-12 · 82026-07-07 · 9

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/mcanouil/nacho on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Coverage (1)

Codecov

Show all practices

Governance and community (3)

Issue templatesFundingSupport guide

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (9)

utilsdata.table ggplot2 ggforce ggrepel knitr rmarkdown shiny shinyWidgets

LinkingTo (0)

none

Suggests (6)

roxygen2 testthat covr Biobase GEOquery limma

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Mickaël Canouil

Author, Maintainer

Authors (3)

Mickaël Canouil

Author, Maintainer

Gerard Bouland

Author

Roderick Slieker

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.6Latest
2024-01-12 · current release · diff ↗
2.0.5
2023-08-07 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.0.4
2023-04-01 · diff ↗
2.0.2
2022-12-06 · diff ↗
2.0.1
2022-11-25 · diff ↗
2.0.0
2022-05-31 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.0
2021-01-14 · diff ↗
1.0.2
2021-01-05 · diff ↗
1.0.1
2020-05-27 · diff ↗
R
R 4.0.0 released · 2020-04-24

Show 8 earlier events

1.0.0
2020-01-09 · diff ↗
0.6.1
2019-10-12 · diff ↗
0.6.0
2019-10-07 · diff ↗
0.5.6
2019-04-29 · diff ↗
unarchivedReturned to CRAN
2019-04-29
0.5.5
2019-04-28
archivedRemoved from CRAN
2019-04-27
policy violation Internet access failures
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-04-28
Total releases: 14 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 41 KB / 1 file
Download size: 2.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Report a problem with this page →