PeakSegJoint

2024.12.4

Joint Peak Detection in Several ChIP-Seq Samples

0packages depend

8.6Kdownloads / year

83.0%test coverage

13/13checks pass

Overview

About

Maintained by Toby Dylan HockingFirst published 2017-08-169 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 2.5 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.47

83.0%

Coverage · measured lines

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

8.6K

CRAN downloads in the past year

Rank #4,876 · ~23/day · ~714/mo

Releases R versions

Daily download trend is not available in this view yet.

45530 days

1.9K90 days

8.6K1 year

Compare downloads with other packages →

Also on399 r2u27 autocran19 c2d4u

Repository

GitHub ↗ tdhock/peaksegjoint

5Stars

2Forks

0Open issues

0Open PRs

0Releases

603Commits

4Contributors

603 commits · Last activity 2024-12-04

Stars over time

2019-05-19 · 52026-07-07 · 5

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/tdhock/peaksegjoint on 2026-07-19.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Toby Dylan Hocking

Author, Maintainer

Authors (1)

Toby Dylan Hocking

Author, Maintainer

Listed in earlier versions (1)

Hocking

no longer listed · 2024.10.1 to 2024.12.4

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2024.12.4Latest
2024-12-04 · current release · diff ↗
2024.10.1
2024-10-02 · diff ↗
2024.6.27
2024-06-27 · diff ↗
R
R 4.4.0 released · 2024-04-24
2024.1.24
2024-01-24 · diff ↗
2023.4.24
2023-04-25 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2022.4.6
2022-04-07 · diff ↗
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
2018.10.3
2018-10-03 · diff ↗
2018.01.09
2018-10-01 · diff ↗

Show 3 earlier events

R
R 3.5.0 released · 2018-04-23
2017.08.11
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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