R Observatory: Metrics for EmbedSOM version 2.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EmbedSOM

2.2.1Package record

Fast Embedding Guided by Self-Organizing Map

0packages depend

6.2Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Mirek KratochvilCRAN page ↗GitHub ↗

Provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. Designed to work with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019) doi:10.12688/f1000research.21642.1.

Install

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

install.packages("EmbedSOM", 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("exaexa/EmbedSOM")

Development version from exaexa/EmbedSOM. 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-embedsom

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-EmbedSOM

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-EmbedSOM

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

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘Matrix’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 3.8 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-04-10
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE5 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

Documentation signals are not tracked yet for this package.

Websitenot declared in DESCRIPTION

Vignettes (1)

EmbedSOM basic embedding HTML

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #4,823 · ~17/day · ~517/mo

EmbedSOM Releases R versions

Daily download trend is not available in this view yet.

58530 days

1.7K90 days

6.2K1 year

Compare downloads with other packages →

Also on392 r2u6 autocran

How downloads are counted

Repository

exaexa/embedsom ↗Account: exaexa

26Stars

5Forks

0Open issues

0Open PRs

2Releases

150Commits

2Commit identities

visualizationsomcytometryrstats

License file reads as GPL-3.0 · 150 commits · Last activity 2026-03-08

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 54
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

Checks run against github.com/exaexa/embedsom on 2026-10-11.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing EmbedSOM adds 43 packages (28 with compiled code, 42 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (1)

R >= 3.2

Imports (6)

ggplot2 igraphMatrixRtsne umap uwot

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (5)

Mirek Kratochvil

Author, Maintainer since 1.9 (2019)

Copyright holder

Copyright holder

Copyright holder

Copyright holder

Releases (6)

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-03-10
2.2.1Latest
record
2026-03-10 · current release · diff ↗
archivedRemoved from CRAN
2025-12-22
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2025-01-31
2.2
record
2025-01-31 · diff ↗
archivedRemoved from CRAN
2025-01-10
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.1.2
record
2022-07-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.1.1
record
2020-02-12 · diff ↗ ·
added 11 exports
ExprColors, GQTSOM, GraphCoords, MSTCoords, RandomMap, UMAPCoords, UMatrixCoords, kMeansMap, kNNCoords, tSNECoords, uwotCoords
1.9.1
record
2019-08-19 · diff ↗

Show 2 earlier eventsHide 2 earlier events

1.9
record
2019-08-19
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-19
Total releases: 6 / 7 yrs
License: GPL (>= 3) OSI
Download size: 235 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("EmbedSOM")

Format

Kratochvil, M., Callebaut, B., Saeys, Y., Van Gassen, S., & Wehrens, R. (2026). EmbedSOM: Fast Embedding Guided by Self-Organizing Map (Version 2.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.EmbedSOM

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 EmbedSOM version 2.2.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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