R Observatory: Metrics for segmenTier version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

segmenTier

0.1.2Package record

Similarity-Based Segmentation of Multidimensional Signals

0packages depend

2.4Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Rainer MachneCRAN page ↗GitHub ↗Issues ↗

A dynamic programming solution to segmentation based on maximization of arbitrary similarity measures within segments. The general idea, theory and this implementation are described in Machne, Murray & Stadler (2017) doi:10.1038/s41598-017-12401-8. In addition to the core algorithm, the package provides time-series processing and clustering functions as described in the publication. These are generally applicable where a `k-means` clustering yields meaningful results, and have been specifically developed for clustering of the Discrete Fourier Transform of periodic gene expression data (`circadian' or `yeast metabolic oscillations'). This clustering approach is outlined in the supplemental material of Machne & Murray (2012) doi:10.1371/journal.pone.0037906), and here is used as a basis of segment similarity measures. Notably, the time-series processing and clustering functions can also be used as stand-alone tools, independent of segmentation, e.g., for transcriptome data already mapped to genes.

Install

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

install.packages("segmenTier", 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("raim/segmenTier")

Development version from raim/segmenTier. 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-segmentier

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-segmenTier

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-segmenTier

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

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Rainer Machne <raim@tbi.univie.ac.at>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Rainer",
                      family = "Machne",
                      role = c("aut", "cre"),
                      email = "raim@tbi.univie.ac.at"),
               person(given = c("Douglas", "B."),
                      family = "Murray",
                      role = "aut"),
               person(given = c("Peter", "F."),
                      family = "Stadler",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 3.7 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.2

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 23includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 27%
Documented parameters: 100%
Return-value docs: 60%
Help pages citing references: 26%

Also includes 2 demo scripts (run with demo())

Vignettes (1)

segmenTier

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #20,946 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

23330 days

63390 days

2.4K1 year

Compare downloads with other packages →

Also on346 r2u7 autocran

How downloads are counted

Repository

raim/segmentier ↗Account: raim

3Stars

1Forks

0Open issues

0Open PRs

1Releases

664Commits

3Commit identities

664 commits · Last activity 2025-07-17

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2021-09-27 · 32026-07-07 · 3

How these are measured

PracticesBeta

Checks run against github.com/raim/segmentier on 2026-10-21.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing segmenTier adds 1 package (1 with compiled code, 1.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB.

Depends (0)

none

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (5)

flowMerge flowClust flowCore knitr rmarkdown

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 (from the free-text Author field) (3)

Rainer Machne

Douglas B. Murray

Peter F. Stadler

Maintainer since 0.1.2 (2019)

Releases (1)

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
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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.1.2Latest
record
2019-02-18 · current release
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-02-18
Total releases: 1 / 7 yrs
License: GPL (>= 2) OSI
Bundled data: 175 KB / 1 file
Download size: 692 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("segmenTier")

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 segmenTier version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →