R Observatory: Metrics for HTSCluster version 2.0.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HTSCluster

2.0.11Package record

Clustering High-Throughput Transcriptome Sequencing (HTS) Data

0packages depend

4.7Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Andrea RauCRAN page ↗

A Poisson mixture model is implemented to cluster genes from high- throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).

Install

R (CRAN)Ubuntu (r2u)

install.packages("HTSCluster", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-htscluster

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

Health

CRAN checks

2NOTE11OK

Check messages

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

Maintainer: ‘Andrea Rau <andrea.rau@jouy.inra.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Andrea",
                      family = "Rau",
                      role = c("aut", "cre"),
                      email = "andrea.rau@jouy.inra.fr"),
               person(given = "Gilles",
                      family = "Celeux",
                      role = "aut"),
               person(given = "Marie-Laure",
                      family = "Martin-Magniette",
                      role = "aut"),
               person(given = c("Cathy", "Maugis-"),
                      family = "Rabusseau",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 1.4 min · r-release-macos-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.11

READMEYes · 70 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structuredCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 11includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 88%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 91%

Vignettes (1)

Co-expression analysis of RNA-seq data with the "HTSCluster" package PDF

How these are measured

Downloads

4.7K

CRAN downloads in the past year

Rank #7,213 · ~13/day · ~391/mo

Releases R versions

Daily download trend is not available in this view yet.

51830 days

1.2K90 days

4.7K1 year

Compare downloads with other packages →

Also on102 r2u933 bioconda35 c2d4u

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing HTSCluster adds 2 packages (0 with compiled code, 338 KB of source tarballs). Heaviest: plotrix 313 KB, capushe 25 KB. 1 more not on CRAN is not measured.

Depends (1)

R >= 2.10.0

Imports (6)

edgeR plotrix capushegrDevicesgraphicsstats

LinkingTo (0)

none

Suggests (2)

HTSFilter Biobase

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (4)

Andrea Rau

Gilles Celeux

Marie-Laure Martin-Magniette

Cathy Maugis- Rabusseau

· added in 2.0.8

Maintainer since 1.0 (2011)

Listed in earlier versions (1)

Cathy Maugis-Rabusseau

no longer listed · 1.0 to 2.0.4

Releases (9)

Pick two releases to compare their code metrics.

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
2.0.11Latest
record
2023-09-05 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
2.0.10
record
2022-08-24 · 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
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
2.0.8
record
2016-05-26 · diff ↗ ·
added 1 export
logLikePoisMix
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
2.0.4
record
2014-08-26 · diff ↗ ·
added 1 export
HTSClusterUsersGuide

Show 9 earlier eventsHide 9 earlier events

2.0.3
record
2014-07-28 · diff ↗ ·
removed 1 export
logLikePoisMix
R
R 3.1.0 released · 2014-04-10
2.0.1
record
2013-12-10 · diff ↗
2.0.0
record
2013-09-25 · diff ↗ ·
added 4 exports
PoisMixClusWrapper, probaPostInit, splitEMInit, highDimensionARI
R
R 3.0.0 released · 2013-04-03
1.1
record
2012-06-11 · diff ↗ ·
added 8 exports
emInit, kmeanInit, logLikePoisMix, logLikePoisMixDiff, PoisMixClus, PoisMixMean, PoisMixSim, probaPost
R
R 2.15.0 released · 2012-03-30
1.0
record
2011-11-07
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2011-11-07
Total releases: 9 / 15 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10.0
Download size: 379 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("HTSCluster")

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

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 HTSCluster version 2.0.11 [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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