R Observatory: Metrics for iDOS version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

iDOS

1.0.1

Integrated Discovery of Oncogenic Signatures

0packages depend

2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Syed HaiderFirst published 2016-07-272 releasesCRAN 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.

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).

Health

CRAN checks

13OK

Slowest check: 54 s · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

1

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

2K

CRAN downloads in the past year

Rank #22,074 · ~5/day · ~166/mo

Releases R versions

Daily download trend is not available in this view yet.

12730 days

50690 days

2K1 year

Compare downloads with other packages →

Also on99 r2u11 autocran

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

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.

Code & Tests

People & History

People (2)

Maintainer (1)

Syed Haider

Author, Maintainer

Authors (2)

Syed Haider

Author, Maintainer

Francesca Buffa

Author · added in 1.0.1

Listed in earlier versions (1)

Francesca M Buffa

no longer listed · 1.0.0

Package Timeline

2 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
1.0.1Latest
2024-03-11 · current release · diff ↗
unarchivedReturned to CRAN
2024-03-11
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
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
Installed size: not tracked yet
With dependencies: not tracked yet

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 is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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