RedeR - Interactive visualization and manipulation of nested networks

RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.

Last updated 24 days ago

guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology

7.03 score 7 packages 102 scripts 492 downloads

RTN - RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

Last updated 24 days ago

transcriptionnetworknetworkinferencenetworkenrichmentgeneregulationgeneexpressiongraphandnetworkgenesetenrichmentgeneticvariability

5.97 score 2 packages 52 scripts 356 downloads

RGraphSpace - A Lightweight Interface Between 'ggplot2' and 'igraph' Objects

Interface to integrate 'igraph' and 'ggplot2' graphics within spatial maps. 'RGraphSpace' implements new geometric objects using 'ggplot2' prototypes, customized for representing large 'igraph' objects in a normalized coordinate system. By scaling shapes and graph elements, 'RGraphSpace' can provide a framework for layered visualizations.

Last updated 11 days ago

5.13 score 1 stars 1 packages 9 scripts 137 downloads

PathwaySpace - Spatial Projection of Network Signals along Geodesic Paths

For a given graph containing vertices, edges, and a signal associated with the vertices, the 'PathwaySpace' package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package then uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' could have various applications, such as visualizing and analyzing network data in a graphical format that highlights the relationships and signal strengths between vertices. It can be particularly useful for understanding the influence of signals through complex networks. By combining graph theory, signal processing, and visualization, the 'PathwaySpace' package provides a novel way of representing and analyzing graph data.

Last updated 11 days ago

bioinformaticsbiological-networksgraph

4.54 score 1 stars 5 scripts 85 downloads

geneplast - Evolutionary and plasticity analysis of orthologous groups

Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.

Last updated 24 days ago

geneticsgeneregulationsystemsbiology

4.11 score 16 scripts 234 downloads

RTNduals - Analysis of co-regulation and inference of 'dual regulons'

RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer 'dual regulons', a new concept that tests whether regulators can co-operate or compete in influencing targets.

Last updated 24 days ago

generegulationgeneexpressionnetworkenrichmentnetworkinferencegraphandnetwork

3.78 score 1 packages 2 scripts 250 downloads