segmenTier

0.1.2

Similarity-Based Segmentation of Multidimensional Signals

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Rainer MachneFirst published 2019-02-181 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 60%
References docs: 26%

Downloads

2.4K

CRAN downloads in the past year

Rank #18,591 · ~7/day · ~199/mo

Releases R versions

Daily download trend is not available in this view yet.

18830 days

63990 days

2.4K1 year

Compare downloads with other packages →

Also on399 r2u29 autocran

Repository

GitHub ↗ raim/segmentier

3Stars

1Forks

0Open issues

0Open PRs

1Releases

664Commits

3Contributors

664 commits · Last activity 2025-07-17

Stars over time

2021-09-27 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

Checks run against github.com/raim/segmentier on 2026-07-19.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 2,643 (56%)Rd 1,170 (25%)C++ 431 (9%)Vignettes 346 (7%)Other 165 (3%)

Code characteristics

Object systems

S35

Cyclomatic complexity: 3.0 median / 26 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

52 15 exported

Complexity

6.6 avg / 26 max

Call network

52 nodes / 40 edges

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (3)

Rainer Machne

no longer listed · 0.1.2

Douglas B. Murray

no longer listed · 0.1.2

Peter F. Stadler

no longer listed · 0.1.2

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

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
Installed size: not tracked yet
With dependencies: not tracked yet

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