R Observatory: Metrics for NACHO version 2.0.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

NACHO

2.0.8Package record

NanoString Quality Control Dashboard

0packages depend

3.9Kdownloads / year

98.1%test coverage

13/13flavors OK

Overview

About

Maintained by Mickaël CanouilCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 2.0.8

Bug Fixes

In inst/app/,
fix: render the help pages from their text, so the app no longer writes to the installed package when R CMD check runs it.
fix: open the help pages of the quality-control metrics, whose links never matched their input names.
In autoplot(),
fix: set the smoothing formula of the "PN" and "NORM" plots, which silences the ggplot2 geom_smooth() message.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 10.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-08
ERROR12 OK, 1 ERROR2026-09-29
OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05

Show 2 earlier changesHide 2 earlier changes

NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.8

READMEYes · 424 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 2.0.8Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 11 (2 internal)includes a package overview page
Examples that run: 100%8 run in a plain check (3 of them under a condition)
Exported functions with examples: 86%
Documented parameters: 100%
Return-value docs: 57%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #7,055 · ~11/day · ~327/mo

Releases R versions

Daily download trend is not available in this view yet.

59530 days

1.2K90 days

3.9K1 year

Compare downloads with other packages →

Also on93 r2u12 autocran2.5K conda_forge71 c2d4u

How downloads are counted

Repository

mcanouil/nacho ↗Account: mcanouil

11Stars

5Forks

0Open issues

1Open PRs

31Releases

770Commits

6Commit identities

nanostringshinyquality-controlnormalisationr-packagerstatsmirnamrna

License file reads as GPL-3.0 · 770 commits · Last activity 2026-10-01 · +10% stars, 30d · Default branch at 2.0.8.9000, ahead of CRAN 2.0.8 (checked 2026-10-11) · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 98%
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-09-12 · 82026-09-28 · 11

How these are measured

PracticesBeta

19 development-tooling and community-health practices detected across 9 families in the upstream repository

Checks run against github.com/mcanouil/nacho on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (7)

Code of conductContributing guideIssue templatesPR templateFundingSupport guide

Funding links: GitHub Sponsors

The repository owner accepts GitHub Sponsors

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-01 · The repository has a site deploy workflow

pkgdown site last built 2026-10-01

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 5 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Automation and maintenance (1)

Dependabot

Lint, format, editor (1)

Lint workflow

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing NACHO adds 56 packages (32 with compiled code, 49 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, bslib 5.6 MB.

Depends (1)

R >= 4.1.0

Imports (10)

utilsdata.table ggplot2 ggforce ggrepel knitr rmarkdown scales shiny shinyWidgets

LinkingTo (0)

none

Suggests (8)

markdown roxygen2 testthat withr covr Biobase GEOquery limma

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Mickaël Canouil

Author, Maintainer since 0.5.5 (2019)

Gerard Bouland

Author

Roderick Slieker

Author

Releases (16)

Pick two releases to compare their code metrics.

2.0.8Latest
record
2026-10-01 · current release · diff ↗
2.0.7
record
2026-09-27 · diff ↗
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
2.0.6
record
2024-01-12 · diff ↗
2.0.5
record
2023-08-07 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.0.4
record
2023-04-01 · diff ↗
2.0.2
record
2022-12-06 · diff ↗
2.0.1
record
2022-11-25 · diff ↗
2.0.0
record
2022-05-31 · diff ↗ ·
removed 12 exports
%>%, :=, .data, as_label, as_name, enquo, enquos, expr, nacho_conflicts, summarize, sym, syms
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.0
record
2021-01-14 · diff ↗
1.0.2
record
2021-01-05 · diff ↗

Show 10 earlier eventsHide 10 earlier events

1.0.1
record
2020-05-27 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.0
record
2020-01-09 · diff ↗ ·
removed 1 export
summarise

added 13 exports
:=, .data, as_label, as_name, check_outliers, deploy, enquo, enquos, expr, load_rcc, nacho_conflicts, sym, syms
0.6.1
record
2019-10-12 · diff ↗
0.6.0
record
2019-10-07 · diff ↗ ·
added 3 exports
%>%, autoplot, render
unarchivedReturned to CRAN
2019-04-29
0.5.6
record
2019-04-29 · diff ↗
0.5.5
record
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: 16 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 41 KB / 1 file
Download size: 2.2 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("NACHO")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btz647.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for NACHO version 2.0.8 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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