R Observatory: Metrics for iDOS version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

iDOS

1.0.1Package record

Integrated Discovery of Oncogenic Signatures

0packages depend

2.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Syed HaiderCRAN page ↗

A method to integrate molecular profiles of cancer patients (gene copy number and mRNA abundance) to identify candidate gain of function alterations. These candidate alterations can be subsequently further tested to discover cancer driver alterations. Briefly, this method tests of genomic correlates of mRNA dysregulation and prioritise those where DNA gains/amplifications are associated with elevated mRNA expression of the same gene. For details see, Haider S et al. (2016) "Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia", Genome Biology, https://pubmed.ncbi.nlm.nih.gov/27358048/.

Install

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

install.packages("iDOS", 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-idos

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

# 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-iDOS

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-iDOS

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 52 s · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMENoVignettesNoNEWSYes · 67% structuredCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 100%9 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #22,384 · ~6/day · ~177/mo

Releases R versions

Daily download trend is not available in this view yet.

19330 days

59690 days

2.1K1 year

Compare downloads with other packages →

Also on67 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing iDOS adds 5 packages (0 with compiled code, 228 KB of source tarballs). Heaviest: formatR 94 KB, VennDiagram 81 KB, lambda.r 25 KB.

Depends (2)

R >= 3.6.0VennDiagram

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Syed Haider

Author, Maintainer since 1.0.0 (2016)

Francesca Buffa

Author · added in 1.0.1

Listed in earlier versions (1)

Francesca M Buffa

no longer listed · 1.0.0

Releases (2)

Pick two releases to compare their code metrics.

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
unarchivedReturned to CRAN
2024-03-11
1.0.1Latest
record
2024-03-11 · current release · diff ↗
archivedRemoved from CRAN
2023-08-18
email to the maintainer is undeliverable
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
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.0.0
record
2016-07-27
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-07-27
Total releases: 2 / 10 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.6.0
Download size: 29 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("iDOS")

Format

Haider, S., & Buffa, F. (2024). iDOS: Integrated Discovery of Oncogenic Signatures (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.iDOS

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 iDOS version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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