R Observatory: Metrics for nandb version 2.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nandb

2.1.1Package record

Number and Brightness Image Analysis

0packages depend

7.2Kdownloads / year

94.9%test coverage

13/13flavors OK

Overview

About

Maintained by Rory NolanCRAN page ↗GitHub ↗Website ↗Issues ↗

Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper doi:10.1093/bioinformatics/btx434. The seminal paper for the technique is Digman et al. 2008 doi:10.1529/biophysj.107.114645. A review of the technique was published in 2017 doi:10.1016/j.ymeth.2017.12.001.

Changes in 2.1.1

BUG FIXES

Prep for new ijtiff::display().

From NEWS.md in the release

Install

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

install.packages("nandb", 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("rorynolan/nandb")

Development version from rorynolan/nandb. 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-nandb

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-nandb

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-nandb

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

Additional issues

donttest

CRAN check page ↗

Slowest check: 5.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-11
ERROR12 OK, 1 ERROR2026-07-10
OK13 OK2026-06-09

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.1

READMEYes · 190 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 2.1.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 25includes a package overview page
Examples that run: 15%3 run in a plain check · 9 only when donttest examples are enabled (R CMD check --as-cran) · 8 never run
Exported functions with examples: 83%
Documented parameters: 99%
Return-value docs: 67%
Help pages citing references: 16%

Vignettes (3)

Batch mode HTML
Brightness timeseries HTML
Calculating brightness with single images HTML

How these are measured

Downloads

7.2K

CRAN downloads in the past year

Rank #6,416 · ~20/day · ~598/mo

Releases R versions

Daily download trend is not available in this view yet.

46130 days

1.3K90 days

7.2K1 year

Compare downloads with other packages →

Also on350 r2u5 autocran

How downloads are counted

Repository

rorynolan/nandb ↗Account: rorynolan

2Stars

1Forks

1Open issues

0Open PRs

7Releases

195Commits

2Commit identities

195 commits · Last activity 2025-01-27 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 185
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2018-04-28 · 22026-07-07 · 2

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/rorynolan/nandb on 2026-10-22.

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 (1)

Code of conduct

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-01-27 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Show all practicesHide 4 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Automation and maintenance (1)

pre-commit

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Installing nandb adds 63 packages (35 with compiled code, 50 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.1

Imports (19)

assertthat autothresholdr BBmisc checkmate (>= 1.9.3)detrendr dplyr filesstrings ggplot2 glue ijtiff magrittr purrr Rcpp reshape2 rlang stringr (>= 1.4)utilsviridis withr

LinkingTo (1)

Rcpp

Suggests (11)

abind covr gridExtra knitr magick matrixStats pacman rmarkdown spelling testthat tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Rory Nolan

Luis Alvarez

Contributor, Copyright holder

Sergi Padilla-Parra

Contributor, Thesis advisor, Copyright holder

Releases (15)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.1.1Latest
record
2025-05-07 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.1.0
record
2021-05-17 · diff ↗
2.0.8
record
2021-04-21 · diff ↗
2.0.7
record
2020-05-08 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.0.6
record
2020-03-16 · diff ↗
2.0.5
record
2019-08-22 · diff ↗
2.0.4
record
2019-07-08 · diff ↗
2.0.3
record
2019-06-28 · diff ↗
2.0.2
record
2019-06-17 · diff ↗

Show 11 earlier eventsHide 11 earlier events

2.0.1
record
2019-05-31 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.0.0
record
2018-11-11 · diff ↗ ·
added 1 export
matrix_raster_plot
1.0.1
record
2018-05-08 · diff ↗
1.0.0
record
2018-04-28 · diff ↗ ·
removed 50 exports
ApplyOnPillars, ArrArrHexPlot, BestTau, Bin2Tiff, Bin2TiffFolder, Brightness, BrightnessPlotFolder, BrightnessTimeSeries, BrightnessTimeSeriesTxtFolder, BrightnessTxtFolder, Brightnesses, Closest, CollapseRanges, CorrectForBleaching, CorrectForBleachingFolder, ExpSmooth, ExpSmoothPillars, ExpSmoothRows, FixLUTError, ForceChannels, GroupClose, KmerArray, KmerPlot, KmerTIFFsFromBrightnessCSVs, KmersFromBrightnesses, KmersFromImage, KmersFromImages, KmersFromImagesFolder, ListPillars, MatrixRasterPlot and 20 more

added 28 exports
brightness, brightness_folder, brightness_img, brightness_timeseries, brightness_timeseries_folder, brightness_ts_img, cc_brightness, cc_brightness_folder, cc_brightness_img, cc_brightness_timeseries, cc_brightness_timeseries_folder, cc_brightness_ts_img, cc_number, cc_number_folder, cc_number_img, cc_number_timeseries, cc_number_timeseries_folder, cc_number_ts_img, cross_var, cross_var_pillars, median_filter, number, number_folder, number_img, number_timeseries, number_timeseries_folder, number_ts_img, smooth_filter
unarchivedReturned to CRAN
2018-04-27
R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2018-01-04
errors were not corrected despite reminders
0.2.1
record
2017-07-11 · diff ↗
0.2.0
record
2017-05-29
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-29
Total releases: 15 / 9 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.1
Download size: 649 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("nandb")

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

It points to 10.1093/bioinformatics/btx434.

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 nandb version 2.1.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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