R Observatory: Metrics for chicane version 0.1.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

chicane

0.1.8Package record

Capture Hi-C Analysis Engine

0packages depend

4.2Kdownloads / year

42.3%test coverage

9/13flavors OK

Overview

About

Maintained by Syed HaiderCRAN page ↗

Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.

Changes in 0.1.8

graceful handling of Gviz-UCSC error when retrieving chromosome lengths in vignettes when using R-4.1.0

From NEWS in the release

Install

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

install.packages("chicane", 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-chicane

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-chicane

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-chicane

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

4NOTE9OK

Check messages

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

Maintainer: ‘Syed Haider <Syed.Haider@icr.ac.uk>’

Additional repositories with no packages:
  http://R-Forge.R-project.org/

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
All declared Imports should be used.

CRAN check page ↗

Slowest check: 11.7 min · r-oldrel-windows-x86_64

Status changes

NOTE9 OK, 4 NOTENow
NOTE8 OK, 6 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.8

READMENoVignettesYes · 2 · dynamicNEWSYes · 33% structured · mentions 0.1.8Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 40
Examples that run: 65%13 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run · 1 hold no code
Exported functions with examples: 71%
Documented parameters: 100%
Return-value docs: 93%
Help pages citing references: 5%

Vignettes (2)

How these are measured

Downloads

4.2K

CRAN downloads in the past year

Rank #9,101 · ~12/day · ~350/mo

Releases R versions

Daily download trend is not available in this view yet.

37230 days

1.1K90 days

4.2K1 year

Compare downloads with other packages →

Also on194 r2u11 autocran

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing chicane adds 59 packages (24 with compiled code, 32 MB of source tarballs). Heaviest: data.table 5.7 MB, bslib 5.6 MB, sass 2.9 MB.

Depends (4)

R >= 3.5.0gamlss.tr gamlss data.table

Imports (8)

MASSstatsforeach doParallel iterators bedr knitr rmarkdown

LinkingTo (0)

none

Suggests (5)

testthat GenomicInteractions GenomicRanges Gviz countreg

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 (5)

Syed Haider

Author, Maintainer since 0.1.7 (2021)

Author

Author

Author

Author

Previously maintained by Erle Holgersen (0.1.0 to 0.1.6).

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-11-06
0.1.8Latest
record
2021-11-06 · current release · diff ↗
archivedRemoved from CRAN
2021-11-01
check problems were not corrected in time
0.1.7
record
2021-09-21 · diff ↗
0.1.6
record
2021-07-25 · diff ↗
0.1.5
record
2021-06-10 · diff ↗
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2021-03-24
archivedRemoved from CRAN
2021-03-24
check problems were not corrected in time BioC package 'GenomicInteractions' not used conditionally
0.1.4
record
2021-03-24 · diff ↗
0.1.3
record
2021-01-13 · diff ↗ ·
added 2 exports
check.model.numerical.fit, get.combination.count

Show 6 earlier eventsHide 6 earlier events

0.1.2
record
2020-07-28 · diff ↗ ·
removed 1 export
make.modelfit.plot

added 9 exports
compare.replicates, convert.standard.format, convert.to.one.based, create.locus.plot, create.modelfit.plot, distance.bin, get.components, get.interaction.id, stratified.enrichment.sample
R
R 4.0.0 released · 2020-04-24
0.1.1
record
2019-10-01 · diff ↗ ·
added 1 export
make.modelfit.plot
R
R 3.6.0 released · 2019-04-26
0.1.0
record
2018-08-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-08-30
Total releases: 9 / 8 yrs
License: GPL-2 OSI
Additional repositories: R-Forge.R-project.org
Minimum R: ≥ 3.5.0
Bundled data: 490 KB / 1 file
Download size: 2.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("chicane")

Format

Haider, S., Dudbridge, F., Fletcher, O., Holgersen, E., & Leavy, O. (2021). chicane: Capture Hi-C Analysis Engine (Version 0.1.8) [Computer software]. https://doi.org/10.32614/CRAN.package.chicane

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 chicane version 0.1.8 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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