R Observatory: Metrics for ChIPtest version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-04-20. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 1.0, its last release before removal.

ChIPtest

1.0

Nonparametric Methods for Identifying Differential Enrichment Regions with ChIP-Seq Data

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Vicky Qian Wu1 releasesCRAN page ↗

Nonparametric Tests to identify the differential enrichment region for two conditions or time-course ChIP-seq data. It includes: data preprocessing function, estimation of a small constant used in hypothesis testing, a kernel-based two sample nonparametric test, two assumption-free two sample nonparametric test.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/ChIPtest/ChIPtest_1.0.tar.gz"
pkgFile <- "ChIPtest_1.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-chiptest

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

# 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-ChIPtest

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

0

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on321 r2u7 autocran

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Other (1)

Vicky Qian Wu ; Kyoung-Jae Won ; Hongzhe Li

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-04-20
issues were not corrected despite reminders
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
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.0
2016-07-20
R
R 3.3.0 released · 2016-05-03

Package metadata

Total releases: 1
License: GPL (>= 2.15.1)
Bundled data: 3.2 KB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ChIPtest")

Format

Li, V. Q. W. ;. K. W. ;. H. (n.d.). ChIPtest: Nonparametric Methods for Identifying Differential Enrichment Regions with ChIP-Seq Data (Version 1.0) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=ChIPtest

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 ChIPtest version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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