R Observatory: Metrics for InterSIM version 2.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

InterSIM

2.3.0Package record

Simulation of Inter-Related Genomic Datasets

2packages depend

4.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Prabhakar ChaliseCRAN page ↗

Generates three inter-related genomic datasets: methylation, gene expression and protein expression having user specified cluster patterns. The simulation utilizes the realistic inter- and intra- relationships from real DNA methylation, mRNA expression and protein expression data from the TCGA ovarian cancer study, Chalise (2016) doi:10.1016/j.cmpb.2016.02.011.

Install

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

install.packages("InterSIM", 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-intersim

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-InterSIM

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.4 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 2.3.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 2includes a package overview page
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 50%

How these are measured

Downloads

4.6K

CRAN downloads in the past year

Rank #5,188 · ~13/day · ~387/mo

Releases R versions

Daily download trend is not available in this view yet.

49730 days

1.6K90 days

4.6K1 year

Compare downloads with other packages →

Also on140 r2u

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing InterSIM adds 33 packages (15 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, colorspace 2.0 MB. 1 more not on CRAN is not measured.

Depends (4)

R >= 3.5.0MASSNMFtools

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Depends 1 · Imports 1

Depends, Imports or LinkingTo, most downloaded first

IntNMF M3JF

How these are counted

Code & Tests

Datasets

People & History

People (3)

Prabhakar Chalise

Author, Maintainer since 2.1 (2016)

Brooke Fridley

Author

Rama Raghavan

Author

Previously maintained by Rama Raghavan (1.0 to 2.0).

Releases (5)

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
2.3.0Latest
record
2025-01-11 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
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
unarchivedReturned to CRAN
2018-07-16
2.2.0
record
2018-07-16 · diff ↗
R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2018-03-02
required archived package 'IntNMF'
R
R 3.4.0 released · 2017-04-21
2.1
record
2016-07-30 · diff ↗
R
R 3.3.0 released · 2016-05-03

Show 3 earlier eventsHide 3 earlier events

2.0
record
2015-12-14 · diff ↗
1.0
record
2015-08-14
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-08-14
Total releases: 5 / 11 yrs
License: GPL
Minimum R: ≥ 3.5.0
Bundled data: 837 KB / 13 files
Download size: 845 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("InterSIM")

Format

Chalise, P., Fridley, B., & Raghavan, R. (2025). InterSIM: Simulation of Inter-Related Genomic Datasets (Version 2.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.InterSIM

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 InterSIM version 2.3.0 [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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