Showing 24 of total 24 results (show query)
thomasp85
tidygraph:A Tidy API for Graph Manipulation
A graph, while not "tidy" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.
Maintained by Thomas Lin Pedersen. Last updated 1 months ago.
graph-algorithmsgraph-manipulationigraphnetwork-analysistidyversecpp
57.3 match 553 stars 14.74 score 4.6k scripts 136 dependents
luukvdmeer
sfnetworks:Tidy Geospatial Networks
Provides a tidy approach to spatial network analysis, in the form of classes and functions that enable a seamless interaction between the network analysis package 'tidygraph' and the spatial analysis package 'sf'.
Maintained by Lucas van der Meer. Last updated 3 months ago.
geospatial-networksnetwork-analysisrspatialsimple-featuresspatial-analysisspatial-data-sciencespatial-networkstidygraphtidyverse
13.5 match 372 stars 9.63 score 332 scripts 6 dependents
bioc
ggkegg:Analyzing and visualizing KEGG information using the grammar of graphics
This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.
Maintained by Noriaki Sato. Last updated 2 months ago.
pathwaysdataimportkeggggplot2ggraphpathwaytidygraphvisualization
11.0 match 224 stars 8.12 score 30 scripts 1 dependentsthomasp85
ggraph:An Implementation of Grammar of Graphics for Graphs and Networks
The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
ggplot-extensionggplot2graph-visualizationnetwork-visualizationvisualizationcpp
5.0 match 1.1k stars 16.96 score 9.2k scripts 111 dependentsbioc
ceRNAnetsim:Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.
Maintained by Selcen Ari Yuka. Last updated 5 months ago.
networkinferencesystemsbiologynetworkgraphandnetworktranscriptomicscernamirnanetwork-biologynetwork-simulatortcgatidygraphtidyverse
11.0 match 4 stars 5.76 score 12 scripts
matt-dray
kevinbacran:Degrees of Separation Between CRAN authors
Calculate the shortest path through a graph network between any two authors listed on CRAN. Analagous to the Six Degrees of Kevin Bacon or Erdos Number. Author X collaborates with author Y; author Z collaborates with Y but not X, therefore the distance from X to Z is two.
Maintained by Matt Dray. Last updated 5 years ago.
graphkevin-baconnetworktidygraph
16.3 match 3 stars 2.18 score 6 scripts
r-causal
ggdag:Analyze and Create Elegant Directed Acyclic Graphs
Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.
Maintained by Malcolm Barrett. Last updated 8 months ago.
causal-inferencedagggplot-extension
2.0 match 443 stars 11.78 score 1.8k scripts 5 dependents
urbananalyst
dodgr:Distances on Directed Graphs
Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.
Maintained by Mark Padgham. Last updated 4 days ago.
distanceopenstreetmaproutershortest-pathsstreet-networkscpp
1.9 match 129 stars 11.53 score 229 scripts 4 dependents
marioangst
motifr:Motif Analysis in Multi-Level Networks
Tools for motif analysis in multi-level networks. Multi-level networks combine multiple networks in one, e.g. social-ecological networks. Motifs are small configurations of nodes and edges (subgraphs) occurring in networks. 'motifr' can visualize multi-level networks, count multi-level network motifs and compare motif occurrences to baseline models. It also identifies contributions of existing or potential edges to motifs to find critical or missing edges. The package is in many parts an R wrapper for the excellent 'SESMotifAnalyser' 'Python' package written by Tim Seppelt.
Maintained by Mario Angst. Last updated 4 years ago.
3.6 match 15 stars 5.43 score 18 scripts
hfgolino
EGAnet:Exploratory Graph Analysis – a Framework for Estimating the Number of Dimensions in Multivariate Data using Network Psychometrics
Implements the Exploratory Graph Analysis (EGA) framework for dimensionality and psychometric assessment. EGA estimates the number of dimensions in psychological data using network estimation methods and community detection algorithms. A bootstrap method is provided to assess the stability of dimensions and items. Fit is evaluated using the Entropy Fit family of indices. Unique Variable Analysis evaluates the extent to which items are locally dependent (or redundant). Network loadings provide similar information to factor loadings and can be used to compute network scores. A bootstrap and permutation approach are available to assess configural and metric invariance. Hierarchical structures can be detected using Hierarchical EGA. Time series and intensive longitudinal data can be analyzed using Dynamic EGA, supporting individual, group, and population level assessments.
Maintained by Hudson Golino. Last updated 8 days ago.
2.0 match 47 stars 7.80 score 61 scripts 1 dependents
kharchenkolab
numbat:Haplotype-Aware CNV Analysis from scRNA-Seq
A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
Maintained by Teng Gao. Last updated 15 days ago.
cancer-genomicscnv-detectionlineage-tracingphylogenysingle-cellsingle-cell-analysissingle-cell-rna-seqspatial-transcriptomicscpp
1.8 match 179 stars 7.41 score 120 scripts
rohelab
vsp:Vintage Sparse PCA for Semi-Parametric Factor Analysis
Provides fast spectral estimation of latent factors in random dot product graphs using the vsp estimator. Under mild assumptions, the vsp estimator is consistent for (degree-corrected) stochastic blockmodels, (degree-corrected) mixed-membership stochastic blockmodels, and degree-corrected overlapping stochastic blockmodels.
Maintained by Alex Hayes. Last updated 4 months ago.
1.7 match 26 stars 6.17 score 19 scripts
overton-group
eHDPrep:Quality Control and Semantic Enrichment of Datasets
A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023) <doi:10.1093/gigascience/giad030>). Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
Maintained by Ian Overton. Last updated 2 years ago.
data-qualityhealth-informaticssemantic-enrichment
1.8 match 8 stars 4.90 score 10 scriptsrohelab
fastRG:Sample Generalized Random Dot Product Graphs in Linear Time
Samples generalized random product graphs, a generalization of a broad class of network models. Given matrices X, S, and Y with with non-negative entries, samples a matrix with expectation X S Y^T and independent Poisson or Bernoulli entries using the fastRG algorithm of Rohe et al. (2017) <https://www.jmlr.org/papers/v19/17-128.html>. The algorithm first samples the number of edges and then puts them down one-by-one. As a result it is O(m) where m is the number of edges, a dramatic improvement over element-wise algorithms that which require O(n^2) operations to sample a random graph, where n is the number of nodes.
Maintained by Alex Hayes. Last updated 7 months ago.
adjacency-matrixgraph-samplinglatent-factors
1.7 match 5 stars 4.52 score 22 scriptskharchenkolab
scistreer:Maximum-Likelihood Perfect Phylogeny Inference at Scale
Fast maximum-likelihood phylogeny inference from noisy single-cell data using the 'ScisTree' algorithm by Yufeng Wu (2019) <doi:10.1093/bioinformatics/btz676>. 'scistreer' provides an 'R' interface and improves speed via 'Rcpp' and 'RcppParallel', making the method applicable to massive single-cell datasets (>10,000 cells).
Maintained by Teng Gao. Last updated 2 years ago.
evolutionphylogeneticssingle-cellcpp
1.6 match 7 stars 4.02 score 2 scripts 1 dependents
ropensci
rmangal:'Mangal' Client
An interface to the 'Mangal' database - a collection of ecological networks. This package includes functions to work with the 'Mangal RESTful API' methods (<https://mangal-interactions.github.io/mangal-api/>).
Maintained by Kevin Cazelles. Last updated 1 years ago.
ecologynetworksfood websinteractionsdata publicationsopen access
1.2 match 14 stars 5.07 score 28 scripts
hypertidy
scgraph:Common Forms for Graph Structures
Provides support for the 'silicate' common form data structure for igraph.
Maintained by Michael D. Sumner. Last updated 6 years ago.
2.3 match 7 stars 2.54 score 10 scripts
rmhogervorst
gephi:Write graph objects to a file format that gephi understands
Sometimes you want to visualize your graph information in 'gephi'. 'Gephi' needs certain column names to make sense of the file. This package writes edge and node information to csv files with correct names so you can read it in easily with gephi. You can also read the files in with igraph/tidygraph. It makes it much easier to switch between R and 'gephi'. This R-package does not interface with the open source network visualisation tool 'gephi' but it writes and reads csv files in a way that 'gephi' expects, reducing the friction when switching between tools.
Maintained by Roel M. Hogervorst. Last updated 3 years ago.
2.2 match 6 stars 2.48 score 7 scripts
statisticsnorway
GISSB:Network Analysis on the Norwegian Road Network
A collection of GIS (Geographic Information System) functions in R, created for use in Statistics Norway. The functions are primarily related to network analysis on the Norwegian road network.
Maintained by Sindre Mikael Haugen. Last updated 19 days ago.
1.1 match 4 stars 4.30 score 8 scripts
gertstulp
FertNet:Process Data from the Social Networks and Fertility Survey
Processes data from The Social Networks and Fertility Survey, downloaded from <https://dataarchive.lissdata.nl>, including correcting respondent errors and transforming network data into network objects to facilitate analyses and visualisation.
Maintained by Gert Stulp. Last updated 10 months ago.
1.6 match 2.70 score 2 scriptshypertidy
activate:Activate to Determine the Context of Subsequent Manipulations
A simple context-controlling mechanism to 'activate' a named sub-entity in an object. The generic functions are provided with bare default methods. It is expected that other packages will import the generic and specialize it.
Maintained by Michael D. Sumner. Last updated 8 years ago.
1.6 match 1 stars 2.18 score 3 scripts 1 dependents
stocnet
migraph:Univariate and Multivariate Tests for Multimodal and Other Networks
A set of tools for testing networks. It includes functions for univariate and multivariate conditional uniform graph and quadratic assignment procedure testing, and network regression. The package is a complement to 'Multimodal Political Networks' (2021, ISBN:9781108985000), and includes various datasets used in the book. Built on the 'manynet' package, all functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode and two-mode (bipartite) networks.
Maintained by James Hollway. Last updated 4 months ago.
igraphmultilevel-networksmultimodal-networknetwork-analysissna
0.5 match 40 stars 6.49 score 33 scriptsstocnet
manynet:Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
Many tools for making, modifying, mapping, marking, measuring, and motifs and memberships of many different types of networks. All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode, two-mode (bipartite), and sometimes three-mode networks. The package includes functions for importing and exporting, creating and generating networks, modifying networks and node and tie attributes, and describing and visualizing networks with sensible defaults.
Maintained by James Hollway. Last updated 2 months ago.
diffusion-modelsgraphsnetwork-analysis
0.5 match 13 stars 6.41 score 35 scripts 1 dependents
urban-sustainability-lab-zurich
diskurs:An R Package To Handle Discourse Network Data
An R package to handle discourse network data as a bipartite graph of actor nodes, qualified stance edges and statement (belief) nodes.
Maintained by Mario Angst. Last updated 6 months ago.
1.8 match 1.70 score 2 scripts