R Observatory: Metrics for integIRTy version 1.0.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

integIRTy

1.0.9Package record

Integrating Multiple Modalities of High Throughput Assays Using Item Response Theory

0packages depend

2.9Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Kevin R. CoombesCRAN page ↗Website ↗

Provides a systematic framework for integrating multiple modalities of assays profiled on the same set of samples. The goal is to identify genes that are altered in cancer either marginally or consistently across different assays. The heterogeneity among different platforms and different samples are automatically adjusted so that the overall alteration magnitude can be accurately inferred. See Tong and Coombes (2012) doi:10.1093/bioinformatics/bts561.

Install

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

install.packages("integIRTy", 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-integirty

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-integIRTy

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-integIRTy

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: 3.4 min · r-oldrel-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 1.0.9

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsiteYes

Help pages: 11
Examples that run: 100%9 run in a plain check
Exported functions with examples: 90%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 91%

Vignettes (1)

integIRTy Vignette PDF

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #10,928 · ~8/day · ~238/mo

Releases R versions

Daily download trend is not available in this view yet.

44730 days

95290 days

2.9K1 year

Compare downloads with other packages →

Also on97 r2u9 autocran51 c2d4u

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing integIRTy adds 22 packages (12 with compiled code, 9.8 MB of source tarballs). Heaviest: mclust 2.7 MB, mvtnorm 1.0 MB, vctrs 1.0 MB.

Depends (4)

R >= 2.10ltm foreach doParallel

Imports (3)

mclustMASSabind

LinkingTo (0)

none

Suggests (1)

KernSmooth

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 (2)

Kevin R. Coombes

Author, Maintainer since 1.0.5 (2017)

Pan Tong

Author

Listed in earlier versions (2)

Kevin R Coombes

no longer listed · 1.0.5 to 1.0.7

Coombes

no longer listed · 1.0.8 to 1.0.9

Releases (5)

Pick two releases to compare their code metrics.

1.0.9Latest
record
2026-09-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.8
record
2025-04-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.7
record
2022-05-03 · diff ↗
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
1.0.6
record
2019-05-06 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.0.5
record
2017-07-11
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-07-11
Total releases: 5 / 9 yrs
License: Apache License (== 2.0)
Minimum R: ≥ 2.10
Bundled data: 649 KB / 1 file
Download size: 1.2 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("integIRTy")

Format

Coombes, K. R., & Tong, P. (2026). integIRTy: Integrating Multiple Modalities of High Throughput Assays Using Item Response Theory (Version 1.0.9) [Computer software]. https://doi.org/10.32614/CRAN.package.integIRTy

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 integIRTy version 1.0.9 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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