R Observatory: Metrics for hicream version 0.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hicream

0.0.4Package record

HIC diffeREntial Analysis Method

0packages depend

2.7Kdownloads / year

–test coverage

10/13flavors OK

Overview

About

Maintained by Elise JorgeCRAN page ↗Repository ↗Website ↗Issues ↗

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.

Changes in 0.0.4

Fixes

fixed a bug related to improper handling of pd.DataFrame in reticulate

From NEWS.md in the release

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. 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

Health

CRAN checks

2ERROR1NOTE10OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package required but not available: ‘diffHic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

NOTEfor detritus in the temp directoryr-devel-linux-x86_64-fedora-gcc

Found the following files/directories:
  ‘uv-setuptools-987040711f7d76f1.lock’

CRAN check page ↗

Slowest check: 10.8 min · r-oldrel-windows-x86_64

Status changes

ERROR10 OK, 1 NOTE, 2 ERRORNow
ERROR10 OK, 4 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.4

READMEYes · 504 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.0.4Citation fileNoWebsiteYes

Help pages: 5
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 20%

Vignettes (2)

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #15,612 · ~7/day · ~224/mo

Releases R versions

Daily download trend is not available in this view yet.

27230 days

78790 days

2.7K1 year

Compare downloads with other packages →

Also on84 r2u

How downloads are counted

Repository

forge.inrae.fr/scales/hicream ↗

1Stars

1Forks

4Open issues

0Open PRs

0Releases

132Commits

6Commit identities

R-packageHi-Cdifferential analysispost hoc inferenceMIAT software

License file reads as GPL-3.0 · 132 commits · Last activity 2026-01-13

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: GitHub only
Median days to close, 50 most recently updated closed PRs: GitHub only

How these are measured

PracticesBeta

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 v3 (2026-09-26)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing hicream adds 64 packages (35 with compiled code, 50 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, dendextend 4.5 MB. 11 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (9)

Elise Jorge

Author, Maintainer since 0.0.1 (2025)

Sylvain Foissac

Author

Toby Hocking

Author · added in 0.0.2

Author

Author

Contributor

Contributor

Nicolas Enjalbert-Courrech

Contributor

Etienne Roquain

Contributor

Releases (4)

Pick two releases to compare their code metrics.

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

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 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 hicream version 0.0.4 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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