R Observatory: Metrics for idiffomix version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

idiffomix

1.0.0Package record

Integrated Differential Analysis of Multi Omics Data using a Joint Mixture Model

0packages depend

2.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Koyel MajumdarCRAN page ↗

A joint mixture model has been developed by Majumdar et al. (2025) doi:10.48550/arXiv.2412.17511 that integrates information from gene expression data and methylation data at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites and differentially expressed genes. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm.

Install

R (CRAN)Ubuntu (r2u)

install.packages("idiffomix", 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-idiffomix

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

13OK

CRAN check page ↗

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
WARNING12 OK, 1 WARNING2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6
Examples that run: 100%3 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

idiffomix: integrated differential analysis of multi-omics data using a joint mixture model HTML

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #18,031 · ~6/day · ~195/mo

Releases R versions

Daily download trend is not available in this view yet.

28530 days

71690 days

2.3K1 year

Compare downloads with other packages →

Also on352 r2u

How downloads are counted

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing idiffomix adds 38 packages (19 with compiled code, 36 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, mclust 2.7 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.5.0

Imports (17)

foreach doParallelparallelmcluststatsutilsedgeR magrittr ggplot2 scales tidyr dplyr reshape2 gridExtragridtidyselect cowplot

LinkingTo (0)

none

Suggests (2)

rmarkdown knitr

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)

Koyel Majumdar

Maintainer since 1.0.0 (2025), Author

Isobel Claire Gorley

Author

Florence Jaffrezic

Author

Thomas Brendan Murphy

Author

Andrea Rau

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.0Latest
record
2025-01-13 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-13
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 13 KB / 3 files
Download size: 94 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("idiffomix")

Format

Majumdar, K., Gorley, I. C., Jaffrezic, F., Murphy, T. B., & Rau, A. (2025). idiffomix: Integrated Differential Analysis of Multi Omics Data using a Joint Mixture Model (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.idiffomix

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 idiffomix version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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