graphsim

1.0.4

Simulate Expression Data from 'igraph' Networks

1packages depend

8.7Kdownloads / year

0.0%test coverage

8/13checks pass

Overview

About

Maintained by S. Thomas KellyFirst published 2020-03-166 releasesCRAN page ↗GitHub ↗

Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.

Install

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

install.packages("graphsim", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("TomKellyGenetics/graphsim")

Development version from TomKellyGenetics/graphsim. Installs pak first if it is not already available.

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-graphsim

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-graphsim

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-graphsim

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 2.5 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.28

0.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 590 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 100%
References docs: 0%

Downloads

8.7K

CRAN downloads in the past year

Rank #6,941 · ~24/day · ~725/mo

Releases R versions

Daily download trend is not available in this view yet.

47930 days

1.4K90 days

8.7K1 year

Compare downloads with other packages →

Also on169 r2u30 autocran23 c2d4u

Repository

GitHub ↗ tomkellygenetics/graphsim

25Stars

7Forks

0Open issues

0Open PRs

9Releases

432Commits

3Contributors

r-statsigraph-networkssimulated-datagraph-algorithmspackagejossgeneticsgene-expression

License GPL-3.0 · 432 commits · Last activity 2025-05-12 · 0% stars, 30d

Stars over time

2024-12-09 · 242026-07-07 · 25

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/tomkellygenetics/graphsim on 2026-07-26.

Continuous integration (3)

Travis CIAppVeyorCircleCI

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Lint, format, editor (1)

RStudio project

Show all practices

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (6)

gplots igraph mvtnorm matrixcalcMatrixgraphics

LinkingTo (0)

none

Suggests (9)

devtools knitr markdown prettydoc R.rsp rmarkdown testthat scales vdiffr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

leiden

Code & Tests

People & History

People (4)

Maintainer (1)

S. Thomas Kelly

Author, Maintainer

Authors (2)

S. Thomas Kelly

Author, Maintainer

Michael A. Black

Author, Thesis advisor

Contributors (2)

Jason Cory Brunson

Contributor · added in 1.0.1

Robrecht Cannoodt

Contributor · added in 1.0.1

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.4Latest
2025-05-13 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.3
2022-09-12 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.2
2021-07-30 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.1
2020-07-17 · diff ↗
1.0.0
2020-07-02 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.2
2020-03-16
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-16
Total releases: 6 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 140 KB / 4 files
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Causal Inference Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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