R Observatory: Metrics for PeakSegJoint version 2024.12.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PeakSegJoint

2024.12.4Package record

Joint Peak Detection in Several ChIP-Seq Samples

0packages depend

7.4Kdownloads / year

83.0%test coverage

13/13flavors OK

Overview

About

Maintained by Toby Dylan HockingCRAN page ↗GitHub ↗Issues ↗

Jointly segment several ChIP-seq samples to find the peaks which are the same and different across samples. The fast approximate maximum Poisson likelihood algorithm is described in "PeakSegJoint: fast supervised peak detection via joint segmentation of multiple count data samples" doi:10.48550/arXiv.1506.01286 by TD Hocking and G Bourque.

Changes in 2024.12.4

update src/profile.c to avoid invalid memory access, thanks CRAN.

From NEWS in the release

Install

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

install.packages("PeakSegJoint", 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("tdhock/PeakSegJoint")

Development version from tdhock/PeakSegJoint. 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-peaksegjoint

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-PeakSegJoint

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-PeakSegJoint

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

CRAN check page ↗

Slowest check: 3.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2024.12.4

READMENoVignettesNoNEWSYes · 100% structured · mentions 2024.12.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 26
Examples that run: 100%11 run in a plain check
Exported functions with examples: 73%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

How these are measured

Downloads

7.4K

CRAN downloads in the past year

Rank #7,219 · ~20/day · ~620/mo

Releases R versions

Daily download trend is not available in this view yet.

42330 days

1.2K90 days

7.4K1 year

Compare downloads with other packages →

Also on364 r2u8 autocran34 c2d4u

How downloads are counted

Repository

tdhock/peaksegjoint ↗Account: tdhock

5Stars

2Forks

0Open issues

0Open PRs

0Releases

603Commits

4Commit identities

603 commits · Last activity 2024-12-04

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 6

Stars over time

2019-05-19 · 52026-07-07 · 5

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/tdhock/peaksegjoint 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

Coverage (1)

Coverage reporting

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing PeakSegJoint adds 20 packages (10 with compiled code, 22 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, penaltyLearning 2.7 MB.

Depends (1)

R >= 2.14

Imports (3)

PeakErrorparallelpenaltyLearning

LinkingTo (0)

none

Suggests (3)

testthat ggplot2 microbenchmark

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 (1)

Toby Dylan Hocking

Author, Maintainer since 2017.08.11 (2017)

Listed in earlier versions (1)

Hocking

no longer listed · 2024.10.1 to 2024.12.4

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
2024.12.4Latest
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2024-12-04 · current release · diff ↗
2024.10.1
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2024-10-02 · diff ↗
2024.6.27
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2024-06-27 · diff ↗
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R 4.4.0 released · 2024-04-24
2024.1.24
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2024-01-24 · diff ↗
2023.4.24
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2023-04-25 · diff ↗
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R 4.3.0 released · 2023-04-21
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R 4.2.0 released · 2022-04-22
2022.4.6
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2022-04-07 · diff ↗
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R 4.1.0 released · 2021-05-18
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R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
2018.10.3
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2018-10-03 · diff ↗
2018.01.09
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2018-10-01 · diff ↗

Show 3 earlier eventsHide 3 earlier events

R
R 3.5.0 released · 2018-04-23
2017.08.11
record
2017-08-16
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-08-16
Total releases: 9 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.14
Bundled data: 787 KB / 10 files
Download size: 760 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PeakSegJoint")

Format

Hocking, T. D. (2024). PeakSegJoint: Joint Peak Detection in Several ChIP-Seq Samples (Version 2024.12.4) [Computer software]. https://doi.org/10.32614/CRAN.package.PeakSegJoint

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 PeakSegJoint version 2024.12.4 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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