R Observatory: Metrics for hicream version 0.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hicream

0.0.4

HIC diffeREntial Analysis Method

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Elise JorgeFirst published 2025-07-254 releasesCRAN page ↗

Perform Hi-C data differential analysis based on pixel-level differential analysis and a post hoc inference strategy to quantify signal in clusters of pixels. Clusters of pixels are obtained through a connectivity-constrained two-dimensional hierarchical clustering.

Install

R (CRAN)Ubuntu (r2u)

install.packages("hicream", 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-hicream

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

Health

CRAN checks

2ERROR11OK

Failing flavors

ERROR r-oldrel-macos-arm64
ERROR r-oldrel-macos-x86_64

Slowest check: 11.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

21

Dependencies · direct

Check history

ERROR2026-03-10
10 OK · 0 NOTE · 0 WARNING · 4 ERROR · 0 FAILURE

Documentation

READMEYes · 504 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 20%

Downloads

2.4K

CRAN downloads in the past year

Rank #15,914 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

22430 days

66390 days

2.4K1 year

Compare downloads with other packages →

Also on108 r2u

Repository

Repository ↗ scales/hicream

Repository practices

Upstream repositoryBeta

Repository forge.inrae.fr/scales/hicream is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.0.0reticulate

Imports (20)

adjclust auk BiocGenerics csaw diffHic dplyr edgeR GenomeInfoDb GenomicRanges InteractionSet limmaMatrixmethodsreshape2 rlang S4VectorsstatsSummarizedExperimentutilsviridis

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

Elise Jorge

Author, Maintainer

Authors (5)

Elise Jorge

Author, Maintainer

Sylvain Foissac

Author

Toby Hocking

Author · added in 0.0.2

Pierre Neuvial

Author

Nathalie Vialaneix

Author

Contributors (4)

Gilles Blanchard

Contributor

Guillermo Durand

Contributor

Nicolas Enjalbert-Courrech

Contributor

Etienne Roquain

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.0.4Latest
2026-01-30 · current release · diff ↗
0.0.3
2026-01-12 · diff ↗
0.0.2
2025-11-19 · diff ↗
0.0.1
2025-07-25
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-25
Total releases: 4 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0.0
Bundled data: 2.3 KB / 1 file
Download size: 725 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hicream")

Format

Jorge, E., Blanchard, G., Durand, G., Enjalbert-Courrech, N., Foissac, S., Hocking, T., Neuvial, P., Roquain, E., & Vialaneix, N. (2026). hicream: HIC diffeREntial Analysis Method (Version 0.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.hicream

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 hicream version 0.0.4 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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