chicane

0.1.8

Capture Hi-C Analysis Engine

0packages depend

4.3Kdownloads / year

42.3%test coverage

11/13checks pass

Overview

About

Maintained by Syed HaiderFirst published 2018-08-309 releasesCRAN 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.

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.

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).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

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

Code health

Yes

Tests · ratio 0.39

42.3%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 70%
Documented parameters: 100%
Return-value docs: 93%
References docs: 5%

Downloads

4.3K

CRAN downloads in the past year

Rank #11,662 · ~12/day · ~354/mo

Releases R versions

Daily download trend is not available in this view yet.

32230 days

88390 days

4.3K1 year

Compare downloads with other packages →

Also on267 r2u36 autocran

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (5)

Maintainer (1)

Syed Haider

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

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
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
0.1.8Latest
2021-11-06 · current release · diff ↗
unarchivedReturned to CRAN
2021-11-06
archivedRemoved from CRAN
2021-11-01
check problems were not corrected in time
0.1.7
2021-09-21 · diff ↗
0.1.6
2021-07-25 · diff ↗
0.1.5
2021-06-10 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.4
2021-03-24 · diff ↗
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
0.1.3
2021-01-13 · diff ↗

Show 6 earlier events

0.1.2
2020-07-28 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.1
2019-10-01 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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