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 18 Sep. 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

downlit  
Syntax Highlighting and Automatic Linking
Syntax highlighting of R code, specifically designed for the needs of 'RMarkdown' packages like 'pk ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
hmeasure  
The H-Measure and Other Scalar Classification Performance Metrics
Classification performance metrics that are derived from the ROC curve of a classifier. The package ...
Download / Learn more Package Citations See dependency  
injectoR  
R Dependency Injection
R dependency injection framework. Dependency injection allows a program design to follow the depend ...
Download / Learn more Package Citations See dependency  
eyelinker  
Import ASC Files from EyeLink Eye Trackers
Imports plain-text ASC data files from EyeLink eye trackers into (relatively) tidy data frames for ...
Download / Learn more Package Citations See dependency  
data360r  
Wrapper for 'TCdata360' and 'Govdata360' API
Makes it easy to engage with the Application Program Interface (API) of the 'TCdata360' and 'Govdat ...
Download / Learn more Package Citations See dependency  

28,565

R Packages

239,283

Dependencies

75,677

Author Associations

28,566

Publication Badges

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