CREAM

1.1.1

Clustering of Genomic Regions Analysis Method

0packages depend

2.4Kdownloads / year

67.4%test coverage

12/13checks pass

Overview

About

Maintained by Benjamin Haibe-KainsFirst published 2017-10-273 releasesCRAN page ↗GitHub ↗

Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach.

Install

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

install.packages("CREAM", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("bhklab/CREAM")

Development version from bhklab/CREAM. Installs pak first if it is not already available.

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-cream

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-CREAM

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-CREAM

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 55 s · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 4.28

67.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 151 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #18,581 · ~7/day · ~200/mo

Releases R versions

Daily download trend is not available in this view yet.

20030 days

59390 days

2.4K1 year

Compare downloads with other packages →

Also on106 r2u2 autocran

Repository

GitHub ↗ bhklab/cream

14Stars

3Forks

2Open issues

0Open PRs

0Releases

93Commits

4Contributors

peak-detectionfunctional-predictionclusteringbiomedical-informatics

93 commits · Last activity 2021-02-11 · 0% stars, 30d

Stars over time

2023-08-27 · 122026-07-07 · 14

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/bhklab/cream on 2026-07-31.

Continuous integration (2)

Travis CIAppVeyor

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

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (1)

R >= 3.3

Imports (2)

statsutils

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Benjamin Haibe-Kains

Author, Maintainer

Authors (4)

Benjamin Haibe-Kains

Author, Maintainer

Victor Kofia

Author

Mathieu Lupien

Author

Seyed Ali Madani Tonekaboni

Author

Package Timeline

3 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
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
1.1.1Latest
2018-06-06 · current release · diff ↗
unarchivedReturned to CRAN
2018-06-06
archivedRemoved from CRAN
2018-05-09
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
1.1.0
2018-01-05 · diff ↗
1.0.0
2017-10-27
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-10-27
Total releases: 3 / 9 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.3
Download size: 35 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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