R Observatory: Metrics for DRomics version 2.6.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DRomics

2.6.3Package record

Dose Response for Omics

0packages depend

4.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Aurelie SiberchicotCRAN page ↗Website ↗

Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Delignette-Muller et al (2023) DOI:10.24072/pcjournal.325 and Larras et al (2018) DOI:10.1021/acs.est.8b04752.

Install

R (CRAN)Ubuntu (r2u)

install.packages("DRomics", 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-dromics

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: 13.2 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.6.3

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 2.6.3Citation fileYes · cites a publicationWebsiteYes

Help pages: 23
Examples that run: 100%23 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 39%

Vignettes (1)

Overview of the DRomics package

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #5,741 · ~14/day · ~412/mo

Releases R versions

Daily download trend is not available in this view yet.

52130 days

1.4K90 days

4.9K1 year

Compare downloads with other packages →

Also on150 r2u56 c2d4u

How downloads are counted

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing DRomics adds 31 packages (15 with compiled code, 29 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB. 3 more not on CRAN are not measured.

Depends (6)

R >= 3.5.0DESeq2grDeviceslimma SummarizedExperimentutils

Imports (5)

ggfortify ggplot2graphicsrlangstats

LinkingTo (0)

none

Suggests (15)

knitrparallelplotly rmarkdown shiny shinyBS shinycssloaders shinyjs shinyWidgets sortable sva svglite testthat VennDiagram withr

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 (4)

Aurelie Siberchicot

Author, Maintainer since 1.0-2 (2019)

Elise Billoir

Author

Marie-Laure Delignette-Muller

Author

Floriane Larras

Contributor

Releases (12)

Pick two releases to compare their code metrics.

2.6.3Latest
record
2026-07-31 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.6-2
record
2024-10-16 · diff ↗
2.6-0
record
2024-09-30 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.5-2
record
2024-01-31 · diff ↗ ·
added 1 export
bmdfilter
R
R 4.3.0 released · 2023-04-21
2.5-0
record
2023-01-24 · diff ↗ ·
added 3 exports
selectgroups, PCAdataplot, formatdata4DRomics
R
R 4.2.0 released · 2022-04-22
2.4-0
record
2022-01-06 · diff ↗
2.3-0
record
2021-10-04 · diff ↗ ·
added 3 exports
trendplot, sensitivityplot, bmdplot
R
R 4.1.0 released · 2021-05-18
2.2-0
record
2021-02-09 · diff ↗ ·
added 2 exports
continuousomicdata, plotfit2pdf
2.1-3
record
2020-09-23 · diff ↗
2.1-2
record
2020-09-22 · diff ↗ ·
added 4 exports
continuousanchoringdata, targetplot, bmdplotwithgradient, ecdfquantileplot

Show 5 earlier eventsHide 5 earlier events

R
R 4.0.0 released · 2020-04-24
2.0-1
record
2019-09-16 · diff ↗ ·
added 6 exports
microarraydata, RNAseqdata, metabolomicdata, bmdboot, ecdfplotwithCI, curvesplot
R
R 3.6.0 released · 2019-04-26
1.0-2
record
2019-01-16
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-01-16
Total releases: 12 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 554 KB / 4 files
Download size: 4.0 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DRomics")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 DRomics version 2.6.3 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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