Other packages > Find by keyword >

graphsim  

Simulate Expression Data from 'igraph' Networks
View on CRAN: Click here


Download and install graphsim package within the R console
Install from CRAN:
install.packages("graphsim")

Install from Github:
library("remotes")
install_github("cran/graphsim")

Install by package version:
library("remotes")
install_version("graphsim", "1.0.3")



Attach the package and use:
library("graphsim")
Maintained by
S. Thomas Kelly
[Scholar Profile | Author Map]
First Published: 2020-03-16
Latest Update: 2022-09-12
Description:
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.
How to cite:
S. Thomas Kelly (2020). graphsim: Simulate Expression Data from 'igraph' Networks. R package version 1.0.3, https://cran.r-project.org/web/packages/graphsim. Accessed 01 May. 2025.
Previous versions and publish date:
0.1.2 (2020-03-16 15:10), 1.0.0 (2020-07-02 09:40), 1.0.1 (2020-07-17 11:50), 1.0.2 (2021-07-30 10:00)
Other packages that cited graphsim R package
View graphsim citation profile
Other R packages that graphsim depends, imports, suggests or enhances
Complete documentation for graphsim
Downloads during the last 30 days
04/0104/0204/0304/0404/0504/0604/0704/0804/0904/1004/1104/1204/1304/1404/1504/1604/1704/1804/1904/2004/2104/2204/2304/2404/2504/2604/2704/2804/2904/30Downloads for graphsim51015202530TrendBars

Today's Hot Picks in Authors and Packages

dsm  
Density Surface Modelling of Distance Sampling Data
Density surface modelling of line transect data. A Generalized Additive Model-based approach is use ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
pander  
An R 'Pandoc' Writer
Contains some functions catching all messages, 'stdout' and other useful information while evaluati ...
Download / Learn more Package Citations See dependency  
representr  
Create Representative Records After Entity Resolution
An implementation of Kaplan, Betancourt, Steorts (2022) that cre ...
Download / Learn more Package Citations See dependency  
geofabrik  
Downloading Open Street Map Data
Download OpenStreetMap data from geofabrik servers httpsdownload.geofabrik.de. This approach usesonl ...
Download / Learn more Package Citations See dependency  
dCUR  
Dimension Reduction with Dynamic CUR
Dynamic CUR (dCUR) boosts the CUR decomposition (Mahoney MW., Drineas P. (2009) ...
Download / Learn more Package Citations See dependency  

24,142

R Packages

207,311

Dependencies

65,176

Author Associations

24,143

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA