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RGraphSpace - Rendering Graphs as Coherent Spatial Objects in 'ggplot2'

An interface for rendering 'igraph' objects as 'ggplot2' graphics within a normalized coordinate space. 'RGraphSpace' implements new geometries that treat a graph as a single coherent object, synchronizing node and edge layers under standard aesthetic mappings. Node features are resolved on demand, supporting high-dimensional data without expanding node tables. Spatial alignment is available at the pixel level, with node coordinates anchored to pixel centers through a half-pixel offset, enabling precise node positioning over external reference frames such as images and maps. Core functionality builds on 'igraph', 'ggplot2', and 'tidygraph'; optional geometry and large raster-background images use 'sf' and 'terra' when installed.

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7.64 score 5 stars 1 dependents 75 scripts 551 downloads

RedeR - Interactive visualization and manipulation of nested networks

RedeR combines an R package 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.

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guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology

6.85 score 6 dependents 99 scripts 796 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.

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transcriptionnetworknetworkinferencenetworkenrichmentgeneregulationgeneexpressiongraphandnetworkgenesetenrichmentgeneticvariability

6.22 score 2 dependents 93 scripts 741 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 uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' has various applications, such as visualizing network data in a graphical format that highlights the relationships and signal strengths between vertices. By combining graph theory, signal processing, and visualization, 'PathwaySpace' provides a way of representing graph data on a continuous projection space. Based on methods introduced in Tercan et al. (2025) <doi:10.1016/j.xpro.2025.103681> and Ellrott et al. (2025) <doi:10.1016/j.ccell.2024.12.002>.

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bioinformaticsbiological-networksgraph

5.90 score 3 stars 25 scripts 501 downloads

TreeAndLeaf - Displaying binary trees with focus on dendrogram leaves

TreeAndLeaf implements a hybrid layout strategy that enhances leaf-level visualization in dendrograms. By integrating force-directed graph and tree layout algorithms, it enables projection of multiple layers of information onto graph–tree diagrams.

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graphandnetworknetworkvisualizationdatarepresentationsoftwaresystemsbiologybinary-treebinary-tree-visualizationdendrogramreorganizing-dendrograms

5.37 score 15 stars 26 scripts 444 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.

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geneticsgeneregulationsystemsbiology

4.23 score 14 scripts 500 downloads

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

RTNduals identifies co-regulatory loops between pairs of regulons inferred by the RTN package by evaluating their shared target genes. It infers dual regulons and tests whether regulator pairs exhibit cooperative or competitive influences on common targets.

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generegulationgeneexpressionnetworkenrichmentnetworkinferencegraphandnetwork

3.95 score 1 dependents 5 scripts 462 downloads