Other packages > Find by keyword >

Patterns  

Deciphering Biological Networks with Patterned Heterogeneous Measurements
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("Patterns", "1.7")



Attach the package and use:
library("Patterns")
Maintained by
Frederic Bertrand
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-06-07
Latest Update: 2025-07-02
Description:
A modeling tool dedicated to biological network modeling (Bertrand and others 2020, ). It allows for single or joint modeling of, for instance, genes and proteins. It starts with the selection of the actors that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its differential measurement (for instance gene expression or protein abundance) or on its time course profile. Wrappers for actors clustering functions and cluster analysis are provided. It also allows reverse engineering of biological networks taking into account the observed time course patterns of the actors. Many inference functions are provided and dedicated to get specific features for the inferred network such as sparsity, robust links, high confidence links or stable through resampling links. Some simulation and prediction tools are also available for cascade networks (Jung and others 2014, ). Example of use with microarray or RNA-Seq data are provided.
How to cite:
Frederic Bertrand (2019). Patterns: Deciphering Biological Networks with Patterned Heterogeneous Measurements. R package version 1.7, https://cran.r-project.org/web/packages/Patterns. Accessed 10 Oct. 2026.
Previous versions and publish date:
(2026-07-09 08:17), 1.0 (2019-06-07 10:10), 1.1 (2019-08-24 06:20), 1.2 (2019-11-13 23:30), 1.3 (2021-03-21 11:00), 1.4 (2022-12-01 14:10), 1.5 (2024-05-06 15:40), 1.6 (2025-07-02 18:50)
Other packages that cited Patterns R package
View Patterns citation profile
Other R packages that Patterns depends, imports, suggests or enhances
Complete documentation for Patterns
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

keyATM  
Keyword Assisted Topic Models
Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the ...
Download / Learn more Package Citations See dependency  
eoR  
Data Management Package (Exposure and Occurrence Data in R)
This data management package provides some helper classes for publicly available data sources (HMD, ...
Download / Learn more Package Citations See dependency  
adespatial  
Multivariate Multiscale Spatial Analysis
Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the us ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
RPEnsemble  
Random Projection Ensemble Classification
Implements the methodology of "Cannings, T. I. and Samworth, R. J. (2017) Random-projection ensemble ...
Download / Learn more Package Citations See dependency  

28,989

R Packages

247,686

Dependencies

76,729

Author Associations

28,990

Publication Badges

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