R-universe search: edge

igraph

igraph:Network Analysis and Visualization

Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

Maintained by Kirill Müller. Last updated 4 hours ago.

complex-networks graph-algorithms graph-theory mathematics network-analysis network-graph fortran libxml2 glpk openblas cpp

148.5 match 584 stars 21.13 score 31k scripts 1.9k dependents

rich-iannone

DiagrammeR:Graph/Network Visualization

Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.

Maintained by Richard Iannone. Last updated 2 months ago.

graph graph-functions network-graph property-graph visualization

140.5 match 1.7k stars 15.29 score 3.8k scripts 86 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 5 days ago.

visualization graphandnetwork thirdpartyclient network

140.0 match 52 stars 13.47 score 628 scripts 17 dependents

thomasp85

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-extension ggplot2 graph-visualization network-visualization visualization cpp

77.3 match 1.1k stars 16.69 score 9.2k scripts 113 dependents

elvanceyhan

pcds:Proximity Catch Digraphs and Their Applications

Contains the functions for construction and visualization of various families of the proximity catch digraphs (PCDs) (see (Ceyhan (2005) ISBN:978-3-639-19063-2), for computing the graph invariants for testing the patterns of segregation and association against complete spatial randomness (CSR) or uniformity in one, two and three dimensional cases. The package also has tools for generating points from these spatial patterns. The graph invariants used in testing spatial point data are the domination number (Ceyhan (2011) <doi:10.1080/03610921003597211>) and arc density (Ceyhan et al. (2006) <doi:10.1016/j.csda.2005.03.002>; Ceyhan et al. (2007) <doi:10.1002/cjs.5550350106>). The PCD families considered are Arc-Slice PCDs, Proportional-Edge PCDs, and Central Similarity PCDs.

Maintained by Elvan Ceyhan. Last updated 2 years ago.

200.7 match 5.80 score 21 scripts 2 dependents

bioc

edge:Extraction of Differential Gene Expression

The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as sva and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.

Maintained by John D. Storey. Last updated 5 months ago.

multiplecomparison differentialexpression timecourse regression geneexpression dataimport

54.5 match 21 stars 7.77 score 62 scripts

bioc

graph:graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Maintained by Bioconductor Package Maintainer. Last updated 13 days ago.

graphandnetwork

34.4 match 11.86 score 764 scripts 339 dependents

statnet

ergm:Fit, Simulate and Diagnose Exponential-Family Models for Networks

An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.

Maintained by Pavel N. Krivitsky. Last updated 22 days ago.

24.8 match 100 stars 15.36 score 1.4k scripts 36 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-networks network-analysis rspatial simple-features spatial-analysis spatial-data-science spatial-networks tidygraph tidyverse

33.3 match 373 stars 11.43 score 332 scripts 7 dependents

skyebend

networkDynamic:Dynamic Extensions for Network Objects

Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.

Maintained by Skye Bender-deMoll. Last updated 4 months ago.

57.5 match 3 stars 6.37 score 132 scripts 11 dependents

cran

network:Classes for Relational Data

Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.

Maintained by Carter T. Butts. Last updated 4 months ago.

47.5 match 3 stars 7.65 score 146 dependents

liamrevell

phytools:Phylogenetic Tools for Comparative Biology (and Other Things)

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Maintained by Liam J. Revell. Last updated 1 months ago.

23.5 match 220 stars 13.84 score 4.8k scripts 77 dependents

bioc

netZooR:Unified methods for the inference and analysis of gene regulatory networks

netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.

Maintained by Tara Eicher. Last updated 13 days ago.

networkinference network generegulation geneexpression transcription microarray graphandnetwork gene-regulatory-network transcription-factors

32.5 match 105 stars 7.98 score

datastorm-open

visNetwork:Network Visualization using 'vis.js' Library

Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

Maintained by Benoit Thieurmel. Last updated 2 years ago.

16.7 match 550 stars 15.25 score 4.1k scripts 196 dependents

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 2 months ago.

graph-algorithms graph-manipulation igraph network-analysis tidyverse cpp

15.3 match 553 stars 14.74 score 4.6k scripts 136 dependents

bioc

CatsCradle:This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.

Maintained by Michael Shapiro. Last updated 15 days ago.

biologicalquestion statisticalmethod geneexpression singlecell transcriptomics spatial

32.8 match 3 stars 6.52 score

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 1 days ago.

openblas cpp

13.4 match 64 stars 15.83 score 13k scripts 599 dependents

cjvanlissa

tidySEM:Tidy Structural Equation Modeling

A tidy workflow for generating, estimating, reporting, and plotting structural equation models using 'lavaan', 'OpenMx', or 'Mplus'. Throughout this workflow, elements of syntax, results, and graphs are represented as 'tidy' data, making them easy to customize. Includes functionality to estimate latent class analyses, and to plot 'dagitty' and 'igraph' objects.

Maintained by Caspar J. van Lissa. Last updated 23 days ago.

19.2 match 58 stars 10.69 score 330 scripts 1 dependents

elvanceyhan

pcds.ugraph:Underlying Graphs of Proximity Catch Digraphs and Their Applications

Contains the functions for construction and visualization of underlying and reflexivity graphs of the three families of the proximity catch digraphs (PCDs) (see (Ceyhan (2005) ISBN:978-3-639-19063-2), and for computing the edge density of these PCD-based graphs which are then used for testing the patterns of segregation and association against complete spatial randomness (CSR)) or uniformity in one and two dimensional cases. The PCD families considered are Arc-Slice PCDs, Proportional-Edge (PE) PCDs (Ceyhan et al. (2006) <doi:10.1016/j.csda.2005.03.002>) and Central Similarity PCDs (Ceyhan et al. (2007) <doi:10.1002/cjs.5550350106>). See also (Ceyhan (2016) <doi:10.1016/j.stamet.2016.07.003> for edge density of the underlying and reflexivity graphs of PE-PCDs. The package also has tools for visualization of PCD-based graphs for one, two, and three dimensional data.

Maintained by Elvan Ceyhan. Last updated 2 years ago.

73.4 match 2.70 score

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.

distance openstreetmap router shortest-paths street-networks cpp

15.5 match 129 stars 11.52 score 229 scripts 4 dependents

gvegayon

rgexf:Build, Import, and Export GEXF Graph Files

Create, read, and write 'GEXF' (Graph Exchange 'XML' Format) graph files (used in 'Gephi' and others). Using the 'XML' package, rgexf allows reading and writing GEXF files, including attributes, 'GEXF' visual attributes (such as color, size, and position), network dynamics (for both edges and nodes), and edges' weights. Users can build/handle graphs element-by-element or massively through data frames, visualize the graph on a web browser through 'gexf-js' (a 'javascript' library), and interact with the 'igraph' package.

Maintained by George Vega Yon. Last updated 5 months ago.

gephi gexf gexf-graph-files social-network xml

22.9 match 27 stars 7.47 score 199 scripts

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 6 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

16.2 match 173 stars 9.65 score 203 scripts 2 dependents

talgalili

dendextend:Extending 'dendrogram' Functionality in R

Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.

Maintained by Tal Galili. Last updated 2 months ago.

8.8 match 154 stars 17.13 score 6.0k scripts 165 dependents

obrl-soil

h3jsr:Access Uber's H3 Library

Provides access to Uber's H3 library for geospatial indexing via its JavaScript transpile 'h3-js' <https://github.com/uber/h3-js> and 'V8' <https://github.com/jeroen/v8>.

Maintained by Lauren OBrien. Last updated 1 years ago.

discrete-global-grids h3 spatial-indexing

17.7 match 67 stars 8.39 score 205 scripts 4 dependents

bioc

KEGGgraph:KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

Maintained by Jitao David Zhang. Last updated 5 months ago.

pathways graphandnetwork visualization kegg

16.2 match 9.09 score 114 scripts 23 dependents

r-spatial

spdep:Spatial Dependence: Weighting Schemes, Statistics

A collection of functions to create spatial weights matrix objects from polygon 'contiguities', from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial 'autocorrelation', including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord' (1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel' general cross product statistic, Empirical Bayes estimates and 'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992) <doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured join count statistics, 'APLE' ('Li 'et al.' ) <doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C' ('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and 'Getis/Ord' G ('Ord' and 'Getis' 1995) <doi:10.1111/j.1538-4632.1995.tb00912.x>, 'saddlepoint' approximations ('Tiefelsdorf' 2002) <doi:10.1111/j.1538-4632.2002.tb01084.x> and exact tests for global and local 'Moran's I' ('Bivand et al.' 2009) <doi:10.1016/j.csda.2008.07.021> and 'LOSH' local indicators of spatial heteroscedasticity ('Ord' and 'Getis') <doi:10.1007/s00168-011-0492-y>. The implementation of most of these measures is described in 'Bivand' and 'Wong' (2018) <doi:10.1007/s11749-018-0599-x>, with further extensions in 'Bivand' (2022) <doi:10.1111/gean.12319>. 'Lagrange' multiplier tests for spatial dependence in linear models are provided ('Anselin et al'. 1996) <doi:10.1016/0166-0462(95)02111-6>, as are 'Rao' score tests for hypothesised spatial 'Durbin' models based on linear models ('Koley' and 'Bera' 2023) <doi:10.1080/17421772.2023.2256810>. A local indicators for categorical data (LICD) implementation based on 'Carrer et al.' (2021) <doi:10.1016/j.jas.2020.105306> and 'Bivand et al.' (2017) <doi:10.1016/j.spasta.2017.03.003> was added in 1.3-7. From 'spdep' and 'spatialreg' versions >= 1.2-1, the model fitting functions previously present in this package are defunct in 'spdep' and may be found in 'spatialreg'.

Maintained by Roger Bivand. Last updated 1 months ago.

spatial-autocorrelation spatial-dependence spatial-weights

7.3 match 131 stars 16.59 score 6.0k scripts 106 dependents

ms609

TreeTools:Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Maintained by Martin R. Smith. Last updated 7 days ago.

evolutionary-biology phylogenetic-trees phylogenetics cpp

12.0 match 23 stars 9.83 score 124 scripts 10 dependents

symbolixau

h3r:Hexagonal Hierarchical Geospatial Indexing System

Provides access to Uber's 'H3' geospatial indexing system via 'h3lib' <https://CRAN.R-project.org/package=h3lib>. 'h3r' is designed to mimic the 'H3' Application Programming Interface (API) <https://h3geo.org/docs/api/indexing/>, so that any function in the API is also available in 'h3r'.

Maintained by David Cooley. Last updated 4 months ago.

25.5 match 5 stars 4.52 score 33 scripts

johncoene

sigmajs:Interface to 'Sigma.js' Graph Visualization Library

Interface to 'sigma.js' graph visualization library including animations, plugins and shiny proxies.

Maintained by John Coene. Last updated 4 years ago.

htmlwidgets network-visualization sigmajs

19.3 match 72 stars 5.92 score 77 scripts

jakobbossek

mcMST:A Toolbox for the Multi-Criteria Minimum Spanning Tree Problem

Algorithms to approximate the Pareto-front of multi-criteria minimum spanning tree problems.

Maintained by Jakob Bossek. Last updated 2 years ago.

evolutionary-algorithms mcmst minimum-spanning-trees multi-objective-optimization spanningtrees

23.4 match 4 stars 4.73 score 27 scripts

ropensci

spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship

Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2019) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.

Maintained by Alec L. Robitaille. Last updated 2 months ago.

animal gps network social spatial

11.0 match 24 stars 9.97 score 145 scripts 3 dependents

hojsgaard

gRim:Graphical Interaction Models

Provides the following types of models: Models for contingency tables (i.e. log-linear models) Graphical Gaussian models for multivariate normal data (i.e. covariance selection models) Mixed interaction models. Documentation about 'gRim' is provided by vignettes included in this package and the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>); see 'citation("gRim")' for details.

Maintained by Søren Højsgaard. Last updated 6 months ago.

openblas cpp

18.6 match 2 stars 5.77 score 74 scripts

briatte

ggnetwork:Geometries to Plot Networks with 'ggplot2'

Geometries to plot network objects with 'ggplot2'.

Maintained by François Briatte. Last updated 9 months ago.

ggplot2 network-visualization

8.9 match 149 stars 11.74 score 766 scripts 15 dependents

rdinnager

phyf:Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs

The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.

Maintained by Russell Dinnage. Last updated 7 months ago.

23.7 match 1 stars 4.20 score 53 scripts 1 dependents

kangy10

DRIP:Discontinuous Regression and Image Processing

A collection of functions that perform jump regression and image analysis such as denoising, deblurring and jump detection. The implemented methods are based on the following research: Qiu, P. (1998) <doi:10.1214/aos/1024691468>, Qiu, P. and Yandell, B. (1997) <doi: 10.1080/10618600.1997.10474746>, Qiu, P. (2009) <doi: 10.1007/s10463-007-0166-9>, Kang, Y. and Qiu, P. (2014) <doi: 10.1080/00401706.2013.844732>, Qiu, P. and Kang, Y. (2015) <doi: 10.5705/ss.2014.054>, Kang, Y., Mukherjee, P.S. and Qiu, P. (2018) <doi: 10.1080/00401706.2017.1415975>, Kang, Y. (2020) <doi: 10.1080/10618600.2019.1665536>.

Maintained by Yicheng Kang. Last updated 4 months ago.

fortran openblas

18.1 match 5.49 score 31 scripts

frbcesab

chessboard:Create Network Connections Based on Chess Moves

Provides functions to work with directed (asymmetric) and undirected (symmetric) spatial networks. It makes the creation of connectivity matrices easier, i.e. a binary matrix of dimension n x n, where n is the number of nodes (sampling units) indicating the presence (1) or the absence (0) of an edge (link) between pairs of nodes. Different network objects can be produced by 'chessboard': node list, neighbor list, edge list, connectivity matrix. It can also produce objects that will be used later in Moran's Eigenvector Maps (Dray et al. (2006) <doi:10.1016/j.ecolmodel.2006.02.015>) and Asymetric Eigenvector Maps (Blanchet et al. (2008) <doi:10.1016/j.ecolmodel.2008.04.001>), methods available in the package 'adespatial' (Dray et al. (2023) <https://CRAN.R-project.org/package=adespatial>). This work is part of the FRB-CESAB working group Bridge <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/bridge/>.

Maintained by Nicolas Casajus. Last updated 1 years ago.

connectivity-matrix directed-networks neighborhood network one-dimensional-networks spatial-networks two-dimensional-networks undirected-networks

20.5 match 4 stars 4.78 score

ludkinm

SBMSplitMerge:Inference for a Generalised SBM with a Split Merge Sampler

Inference in a Bayesian framework for a generalised stochastic block model. The generalised stochastic block model (SBM) can capture group structure in network data without requiring conjugate priors on the edge-states. Two sampling methods are provided to perform inference on edge parameters and block structure: a split-merge Markov chain Monte Carlo algorithm and a Dirichlet process sampler. Green, Richardson (2001) <doi:10.1111/1467-9469.00242>; Neal (2000) <doi:10.1080/10618600.2000.10474879>; Ludkin (2019) <arXiv:1909.09421>.

Maintained by Matthew Ludkin. Last updated 5 years ago.

35.1 match 2.70 score 3 scripts

pik-piam

edgeTransport:Prepare EDGE Transport Data for the REMIND model

EDGE-T is a fork of the GCAM transport module https://jgcri.github.io/gcam-doc/energy.html#transportation with a high level of detail in its representation of technological and modal options. It is a partial equilibrium model with a nested multinomial logit structure and relies on the modified logit formulation. Most of the sources are not publicly available. PIK-internal users can find the sources in the distributed file system in the folder `/p/projects/rd3mod/inputdata/sources/EDGE-Transport-Standalone`.

Maintained by Johanna Hoppe. Last updated 3 days ago.

13.7 match 5 stars 6.84 score 16 scripts 2 dependents

jtextor

dagitty:Graphical Analysis of Structural Causal Models

A port of the web-based software 'DAGitty', available at <https://dagitty.net>, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.

Maintained by Johannes Textor. Last updated 4 months ago.

7.3 match 302 stars 12.83 score 1.7k scripts 11 dependents

bioc

RCX:R package implementing the Cytoscape Exchange (CX) format

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

Maintained by Florian Auer. Last updated 5 months ago.

pathways dataimport network

14.7 match 8 stars 6.28 score 10 scripts 1 dependents

sem-in-r

seminr:Building and Estimating Structural Equation Models

A powerful, easy to syntax for specifying and estimating complex Structural Equation Models. Models can be estimated using Partial Least Squares Path Modeling or Covariance-Based Structural Equation Modeling or covariance based Confirmatory Factor Analysis. Methods described in Ray, Danks, and Valdez (2021).

Maintained by Nicholas Patrick Danks. Last updated 3 years ago.

common-factors composites construct pls-models

12.3 match 62 stars 7.46 score 284 scripts

asgr

imager:Image Processing Library Based on 'CImg'

Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.

Maintained by Aaron Robotham. Last updated 8 days ago.

libx11 fftw3 tiff cpp openmp

6.7 match 17 stars 13.53 score 2.4k scripts 44 dependents

schochastics

edgebundle:Algorithms for Bundling Edges in Networks and Visualizing Flow and Metro Maps

Implements several algorithms for bundling edges in networks and flow and metro map layouts. This includes force directed edge bundling <doi:10.1111/j.1467-8659.2009.01450.x>, a flow algorithm based on Steiner trees<doi:10.1080/15230406.2018.1437359> and a multicriteria optimization method for metro map layouts <doi:10.1109/TVCG.2010.24>.

Maintained by David Schoch. Last updated 6 months ago.

graph-algorithms network-analysis visualization cpp

13.7 match 129 stars 6.52 score 512 scripts

martin-borkovec

ggparty:'ggplot' Visualizations for the 'partykit' Package

Extends 'ggplot2' functionality to the 'partykit' package. 'ggparty' provides the necessary tools to create clearly structured and highly customizable visualizations for tree-objects of the class 'party'.

Maintained by Martin Borkovec. Last updated 6 years ago.

9.3 match 147 stars 9.48 score 156 scripts 7 dependents

sfcheung

semptools:Customizing Structural Equation Modelling Plots

Most function focus on specific ways to customize a graph. They use a 'qgraph' output as the first argument, and return a modified 'qgraph' object. This allows the functions to be chained by a pipe operator.

Maintained by Shu Fai Cheung. Last updated 3 months ago.

diagram graph lavaan plot sem structural-equation-modeling

12.0 match 7 stars 7.12 score 87 scripts

spatstat

spatstat.explore:Exploratory Data Analysis for the 'spatstat' Family

Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.

Maintained by Adrian Baddeley. Last updated 12 days ago.

cluster-detection confidence-intervals hypothesis-testing k-function roc-curves scan-statistics significance-testing simulation-envelopes spatial-analysis spatial-data-analysis spatial-sharpening spatial-smoothing spatial-statistics

8.4 match 1 stars 10.18 score 67 scripts 150 dependents

alextkalinka

linkcomm:Tools for Generating, Visualizing, and Analysing Link Communities in Networks

Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type. The linkcomm package also includes tools for generating, visualizing, and analysing Overlapping Cluster Generator (OCG) communities. Kalinka and Tomancak (2011) <doi:10.1093/bioinformatics/btr311>.

Maintained by Alex T. Kalinka. Last updated 4 years ago.

clustering networks networks-biology visualization cpp

11.3 match 7 stars 7.53 score 115 scripts 4 dependents

epimodel

EpiModel:Mathematical Modeling of Infectious Disease Dynamics

Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).

Maintained by Samuel Jenness. Last updated 2 months ago.

agent-based-modeling epidemics epidemiology infectious-diseases network-graph cpp

7.3 match 250 stars 11.43 score 315 scripts

bioc

Rgraphviz:Provides plotting capabilities for R graph objects

Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.

Maintained by Kasper Daniel Hansen. Last updated 6 days ago.

graphandnetwork visualization zlib

7.1 match 11.51 score 1.2k scripts 107 dependents

bnosac

image.CannyEdges:Implementation of the Canny Edge Detector for Images

An implementation of the Canny Edge Detector for detecting edges in images. The package provides an interface to the algorithm available at <https://github.com/Neseb/canny>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf fftw3 cpp

16.0 match 278 stars 5.14 score 6 scripts

spatstat

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)

Maintained by Adrian Baddeley. Last updated 7 days ago.

classes-and-objects distance-calculation geometry geometry-processing images mensuration plotting point-patterns spatial-data spatial-data-analysis

6.8 match 7 stars 12.14 score 241 scripts 229 dependents

klausvigo

phangorn:Phylogenetic Reconstruction and Analysis

Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).

Maintained by Klaus Schliep. Last updated 4 days ago.

software technology qualitycontrol phylogenetic-analysis phylogenetics openblas cpp

4.9 match 206 stars 16.70 score 2.5k scripts 135 dependents

bioc

BioNERO:Biological Network Reconstruction Omnibus

BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.

Maintained by Fabricio Almeida-Silva. Last updated 5 months ago.

software geneexpression generegulation systemsbiology graphandnetwork preprocessing network networkinference

10.4 match 27 stars 7.69 score 50 scripts 1 dependents

fmichonneau

phylobase:Base Package for Phylogenetic Structures and Comparative Data

Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

Maintained by Francois Michonneau. Last updated 1 years ago.

phylogenetics cpp

7.1 match 18 stars 11.10 score 394 scripts 18 dependents

garthtarr

edgebundleR:Circle Plot with Bundled Edges

Generates interactive circle plots with the nodes around the circumference and linkages between the connected nodes using hierarchical edge bundling via the D3 JavaScript library. See <http://d3js.org/> for more information on D3.

Maintained by Garth Tarr. Last updated 2 years ago.

10.9 match 70 stars 7.24 score 55 scripts

cbhurley

PairViz:Visualization using Graph Traversal

Improving graphics by ameliorating order effects, using Eulerian tours and Hamiltonian decompositions of graphs. References for the methods presented here are C.B. Hurley and R.W. Oldford (2010) <doi:10.1198/jcgs.2010.09136> and C.B. Hurley and R.W. Oldford (2011) <doi:10.1007/s00180-011-0229-5>.

Maintained by Catherine Hurley. Last updated 3 years ago.

13.4 match 1 stars 5.75 score 42 scripts 3 dependents

frankkramer-lab

mully:Create, Modify and Visualize Multi-Layered Networks

Allows the user to create graphs with multiple layers. The user can also modify the layers, the nodes, and the edges. The graph can also be visualized. Zaynab Hammoud and Frank Kramer (2018) <doi:10.3390/genes9110519>. More about multilayered graphs and their usage can be found in our review paper: Zaynab Hammoud and Frank Kramer (2020) <doi:10.1186/s41044-020-00046-0>.

Maintained by Zaynab Hammoud. Last updated 2 years ago.

big-networks data-visualization graph-theory graphs igraph multilayer-networks node-colored-graphs

12.8 match 45 stars 5.95 score 6 scripts

seninp-bioinfo

MetaComp:EDGE Taxonomy Assignments Visualization

Implements routines for metagenome sample taxonomy assignments collection, aggregation, and visualization. Accepts the EDGE-formatted output from GOTTCHA/GOTTCHA2, BWA, Kraken, MetaPhlAn, DIAMOND, and Pangia. Produces SVG and PDF heatmap-like plots comparing taxa abundances across projects.

Maintained by Pavel Senin. Last updated 7 years ago.

bioinformatics comparative-genomics edge heatmap metagenomics visualization

20.7 match 4 stars 3.60 score 7 scripts

bioc

Mergeomics:Integrative network analysis of omics data

The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).

Maintained by Zeyneb Kurt. Last updated 5 months ago.

software

17.4 match 4.30 score 8 scripts

hojsgaard

gRbase:A Package for Graphical Modelling in R

The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details.

Maintained by Søren Højsgaard. Last updated 5 months ago.

openblas cpp

8.0 match 3 stars 9.24 score 241 scripts 20 dependents

zarquon42b

Rvcg:Manipulations of Triangular Meshes Based on the 'VCGLIB' API

Operations on triangular meshes based on 'VCGLIB'. This package integrates nicely with the R-package 'rgl' to render the meshes processed by 'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI <https://vcg.isti.cnr.it/>, like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk <https://github.com/cnr-isti-vclab/vcglib> and patched to work with options determined by the configure script as well as to work with the header files included by 'RcppEigen'.

Maintained by Stefan Schlager. Last updated 5 months ago.

cpp openmp

7.3 match 25 stars 10.20 score 195 scripts 29 dependents

graemetlloyd

Claddis:Measuring Morphological Diversity and Evolutionary Tempo

Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014) <doi:10.1016/j.cub.2014.08.034>, Close et al. (2015) <doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>, and calculate_morphological_distances(), which implements multiple discrete character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>. Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree() implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and plot_morphospace_stack() implements Foote (1993) <doi:10.1017/S0094837300015864>. Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) <doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>. calculate_tree_length() and reconstruct_ancestral_states() implements the generalised algorithms from Swofford and Maddison (1992; no doi).

Maintained by Graeme T. Lloyd. Last updated 7 days ago.

9.3 match 13 stars 7.86 score 77 scripts 2 dependents

gaborcsardi

simplegraph:Simple Graph Data Types and Basic Algorithms

Simple classic graph algorithms for simple graph classes. Graphs may possess vertex and edge attributes. 'simplegraph' has no dependencies and it is written entirely in R, so it is easy to install.

Maintained by Gabor Csardi. Last updated 2 years ago.

17.2 match 2 stars 4.19 score 26 scripts 1 dependents

christopherkenny

geomander:Geographic Tools for Studying Gerrymandering

A compilation of tools to complete common tasks for studying gerrymandering. This focuses on the geographic tool side of common problems, such as linking different levels of spatial units or estimating how to break up units. Functions exist for creating redistricting-focused data for the US.

Maintained by Christopher T. Kenny. Last updated 1 months ago.

cpp

9.2 match 14 stars 7.81 score 191 scripts 1 dependents

mplex

multiplex:Algebraic Tools for the Analysis of Multiple Social Networks

Algebraic procedures for analyses of multiple social networks are delivered with this package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. 'multiplex' makes possible, among other things, to create and manipulate multiplex, multimode, and multilevel network data with different formats. Effective ways are available to treat multiple networks with routines that combine algebraic systems like the partially ordered semigroup with decomposition procedures or semiring structures with the relational bundles occurring in different types of multivariate networks. 'multiplex' provides also an algebraic approach for affiliation networks through Galois derivations between families of the pairs of subsets in the two domains of the network with visualization options.

Maintained by Antonio Rivero Ostoic. Last updated 2 months ago.

algebra network-analysis semigroup semiring

8.8 match 23 stars 7.98 score 69 scripts 2 dependents

bioc

KEGGlincs:Visualize all edges within a KEGG pathway and overlay LINCS data

See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

Maintained by Shana White. Last updated 5 months ago.

networkinference geneexpression datarepresentation thirdpartyclient cellbiology graphandnetwork pathways kegg network

17.0 match 4.00 score 3 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-inference dag ggplot-extension

5.7 match 443 stars 11.78 score 1.8k scripts 5 dependents

pik-piam

mrremind:MadRat REMIND Input Data Package

The mrremind packages contains data preprocessing for the REMIND model.

Maintained by Lavinia Baumstark. Last updated 4 days ago.

10.3 match 4 stars 6.25 score 15 scripts 1 dependents

skembel

picante:Integrating Phylogenies and Ecology

Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.

Maintained by Steven W. Kembel. Last updated 2 years ago.

5.6 match 34 stars 11.42 score 1.1k scripts 16 dependents

statnet

tsna:Tools for Temporal Social Network Analysis

Temporal SNA tools for continuous- and discrete-time longitudinal networks having vertex, edge, and attribute dynamics stored in the 'networkDynamic' format. This work was supported by grant R01HD68395 from the National Institute of Health.

Maintained by Skye Bender-deMoll. Last updated 1 years ago.

8.3 match 7 stars 7.65 score 93 scripts 2 dependents

adeverse

adespatial:Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Maintained by Aurélie Siberchicot. Last updated 15 hours ago.

fortran openblas

5.6 match 36 stars 11.25 score 398 scripts 2 dependents

sonsoleslp

tna:Transition Network Analysis (TNA)

Provides tools for performing Transition Network Analysis (TNA) to study relational dynamics, including functions for building and plotting TNA models, calculating centrality measures, and identifying dominant events and patterns. TNA statistical techniques (e.g., bootstrapping and permutation tests) ensure the reliability of observed insights and confirm that identified dynamics are meaningful. See (Saqr et al., 2025) <doi:10.1145/3706468.3706513> for more details on TNA.

Maintained by Sonsoles López-Pernas. Last updated 6 days ago.

educational-data-mining learning-analytics markov-model temporal-analysis

9.3 match 4 stars 6.51 score 5 scripts

josherrickson

rlemon:R Access to LEMON Graph Algorithms

Allows easy access to the LEMON Graph Library set of algorithms, written in C++. See the LEMON project page at <https://lemon.cs.elte.hu/trac/lemon>. Current LEMON version is 1.3.1.

Maintained by Josh Errickson. Last updated 2 months ago.

cpp

8.3 match 8 stars 7.04 score 1 scripts 15 dependents

ajsims1704

rdecision:Decision Analytic Modelling in Health Economics

Classes and functions for modelling health care interventions using decision trees and semi-Markov models. Mechanisms are provided for associating an uncertainty distribution with each source variable and for ensuring transparency of the mathematical relationships between variables. The package terminology follows Briggs "Decision Modelling for Health Economic Evaluation" (2006, ISBN:978-0-19-852662-9).

Maintained by Andrew Sims. Last updated 2 months ago.

9.1 match 3 stars 6.46 score 22 scripts

pepijn-devries

ggsankeyfier:Create Sankey and Alluvial Diagrams Using 'ggplot2'

Sankey and alluvial diagrams visualise flows of quantities across stages in stacked bars. This package makes it easy to create such diagrams using 'ggplot2'.

Maintained by Pepijn de Vries. Last updated 7 months ago.

ggplot2 visualisation

8.2 match 17 stars 7.00 score 59 scripts

bioc

flowGraph:Identifying differential cell populations in flow cytometry data accounting for marker frequency

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

Maintained by Alice Yue. Last updated 5 months ago.

flowcytometry statisticalmethod immunooncology software cellbasedassays visualization

13.9 match 4.00 score 10 scripts

lucaweihs

SEMID:Identifiability of Linear Structural Equation Models

Provides routines to check identifiability or non-identifiability of linear structural equation models as described in Drton, Foygel, and Sullivant (2011) <doi:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012) <doi:10.1214/12-AOS1012>, and other works. The routines are based on the graphical representation of structural equation models.

Maintained by Nils Sturma. Last updated 2 years ago.

13.7 match 4 stars 4.06 score 29 scripts

wraff

wrMisc:Analyze Experimental High-Throughput (Omics) Data

The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Other functions help aligning a matrix or data.frame to a reference using partial matching or to mine an experimental setup to extract patterns of replicate samples. Many times large experimental datasets need some additional filtering, adequate functions are provided. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too. Batch reading (or writing) of sets of files and combining data to arrays is supported, too.

Maintained by Wolfgang Raffelsberger. Last updated 7 months ago.

13.1 match 4.23 score 33 scripts 4 dependents

cwatson

brainGraph:Graph Theory Analysis of Brain MRI Data

A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.

Maintained by Christopher G. Watson. Last updated 1 years ago.

brain-connectivity brain-imaging complex-networks connectome connectomics fmri graph-theory mri network-analysis neuroimaging neuroscience statistics tractography

7.0 match 188 stars 7.86 score 107 scripts 3 dependents

evolecolgroup

geoGraph:Walking through the geographic space using graphs

Classes and methods for spatial graphs interfaced with support for GIS shapefiles.

Maintained by Andrea Manica. Last updated 25 days ago.

16.5 match 4 stars 3.30 score 2 scripts

bioc

OmnipathR:OmniPath web service client and more

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Maintained by Denes Turei. Last updated 1 months ago.

graphandnetwork network pathways software thirdpartyclient dataimport datarepresentation genesignaling generegulation systemsbiology transcriptomics singlecell annotation kegg complexes enzyme-ptm networks networks-biology omnipath proteins quarto

5.4 match 130 stars 9.90 score 226 scripts 2 dependents

jakobbossek

grapherator:A Modular Multi-Step Graph Generator

Set of functions for step-wise generation of (weighted) graphs. Aimed for research in the field of single- and multi-objective combinatorial optimization. Graphs are generated adding nodes, edges and weights. Each step may be repeated multiple times with different predefined and custom generators resulting in high flexibility regarding the graph topology and structure of edge weights.

Maintained by Jakob Bossek. Last updated 4 years ago.

combinatorial-optimization graph-generator minimum-spanning-tree multi-objective-optimization optimization

8.5 match 9 stars 6.04 score 27 scripts 1 dependents

tguillerme

dispRity:Measuring Disparity

A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.

Maintained by Thomas Guillerme. Last updated 14 days ago.

disparity ecology multidimensionality palaeobiology

5.8 match 26 stars 8.65 score 220 scripts 1 dependents

epimodel

networkLite:An Simplified Implementation of the 'network' Package Functionality

An implementation of some of the core 'network' package functionality based on a simplified data structure that is faster in many research applications. This package is designed for back-end use in the 'statnet' family of packages, including 'EpiModel'. Support is provided for binary and weighted, directed and undirected, bipartite and unipartite networks; no current support for multigraphs, hypergraphs, or loops.

Maintained by Samuel Jenness. Last updated 25 days ago.

7.7 match 3 stars 6.40 score 1 scripts 13 dependents

gaospecial

ggVennDiagram:A 'ggplot2' Implement of Venn Diagram

Easy-to-use functions to generate 2-7 sets Venn or upset plot in publication quality. 'ggVennDiagram' plot Venn or upset using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in four components, set edges/labels, and region edges/labels. From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar. From version 1.4.4, it supports unlimited number of sets, as it can draw a plain upset plot automatically when number of sets is more than 7.

Maintained by Chun-Hui Gao. Last updated 5 months ago.

set-operations upset upsetplot venn-diagram venn-plot

4.0 match 292 stars 12.31 score 1.3k scripts 4 dependents

donaldrwilliams

GGMncv:Gaussian Graphical Models with Nonconvex Regularization

Estimate Gaussian graphical models with nonconvex penalties <doi:10.31234/osf.io/ad57p>, including the atan Wang and Zhu (2016) <doi:10.1155/2016/6495417>, seamless L0 Dicker, Huang, and Lin (2013) <doi:10.5705/ss.2011.074>, exponential Wang, Fan, and Zhu <doi:10.1007/s10463-016-0588-3>, smooth integration of counting and absolute deviation Lv and Fan (2009) <doi:10.1214/09-AOS683>, logarithm Mazumder, Friedman, and Hastie (2011) <doi:10.1198/jasa.2011.tm09738>, Lq, smoothly clipped absolute deviation Fan and Li (2001) <doi:10.1198/016214501753382273>, and minimax concave penalty Zhang (2010) <doi:10.1214/09-AOS729>. There are also extensions for computing variable inclusion probabilities, multiple regression coefficients, and statistical inference <doi:10.1214/15-EJS1031>.

Maintained by Donald Williams. Last updated 3 years ago.

openblas cpp

7.8 match 5 stars 6.22 score 22 scripts 2 dependents

cran

bnlearn:Bayesian Network Structure Learning, Parameter Learning and Inference

Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.

Maintained by Marco Scutari. Last updated 3 months ago.

openblas

6.3 match 57 stars 7.72 score 32 dependents

kharchenkolab

conos:Clustering on Network of Samples

Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.

Maintained by Evan Biederstedt. Last updated 1 years ago.

batch-correction scrna-seq single-cell-rna-seq openblas cpp openmp

6.6 match 205 stars 7.33 score 258 scripts

diegosasso

ontophylo:Ontology-Informed Phylogenetic Comparative Analyses

This package provides new phylogenetic tools for analyzing discrete trait data integrating bio-ontologies and phylogenetics. It expands on the previous work of Tarasov et al. (2019). The PARAMO pipeline allows to reconstruct ancestral phenomes treating groups of morphological traits as a single complex character. The pipeline incorporates knowledge from ontologies during the amalgamation of individual character stochastic maps. Here we expand the current PARAMO functionality by adding new statistical methods for inferring evolutionary phenome dynamics using non-homogeneous Poisson process (NHPP). The new functionalities include: (1) reconstruction of evolutionary rate shifts of phenomes across lineages and time; (2) reconstruction of morphospace dynamics through time; and (3) estimation of rates of phenome evolution at different levels of anatomical hierarchy (e.g., entire body or specific regions only). The package also includes user-friendly tools for visualizing evolutionary rates of different anatomical regions using PNG vector images of the organisms of interest.

Maintained by Diego S. Porto. Last updated 1 years ago.

17.7 match 1 stars 2.70 score 8 scripts

tdhock

directlabels:Direct Labels for Multicolor Plots

An extensible framework for automatically placing direct labels onto multicolor 'lattice' or 'ggplot2' plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method.

Maintained by Toby Dylan Hocking. Last updated 12 months ago.

4.5 match 83 stars 10.62 score 1.8k scripts 16 dependents

icosa-grid

icosa:Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra

Implementation of icosahedral grids in three dimensions. The spherical-triangular tessellation can be set to create grids with custom resolutions. Both the primary triangular and their inverted penta-hexagonal grids can be calculated. Additional functions are provided that allow plotting of the grids and associated data, the interaction of the grids with other raster and vector objects, and treating the grids as a graphs.

Maintained by Adam T. Kocsis. Last updated 8 months ago.

grid cpp

8.8 match 4 stars 5.41 score 65 scripts

mikehellstern

netgsa:Network-Based Gene Set Analysis

Carry out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>

Maintained by Michael Hellstern. Last updated 3 years ago.

cpp

12.6 match 4 stars 3.75 score 28 scripts

bioc

CIMICE:CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction.

Maintained by Nicolò Rossi. Last updated 5 months ago.

software biologicalquestion networkinference researchfield phylogenetics statisticalmethod graphandnetwork technology singlecell

10.9 match 4.30 score 5 scripts

connordonegan

geostan:Bayesian Spatial Analysis

For spatial data analysis; provides exploratory spatial analysis tools, spatial regression, spatial econometric, and disease mapping models, model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health monitoring data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.

Maintained by Connor Donegan. Last updated 4 months ago.

bayesian bayesian-inference bayesian-statistics epidemiology modeling public-health rspatial spatial stan cpp

5.3 match 80 stars 8.80 score 46 scripts

bioc

PROPS:PRObabilistic Pathway Score (PROPS)

This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.

Maintained by Lichy Han. Last updated 4 months ago.

classification bayesian geneexpression

7.4 match 6.19 score 518 scripts

christophergandrud

networkD3:D3 JavaScript Network Graphs from R

Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.

Maintained by Christopher Gandrud. Last updated 6 years ago.

d3js networks

3.3 match 654 stars 13.60 score 3.4k scripts 31 dependents

statnet

ergm.count:Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges

A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.

Maintained by Pavel N. Krivitsky. Last updated 5 months ago.

5.0 match 10 stars 8.78 score 140 scripts 1 dependents

usccana

netdiffuseR:Analysis of Diffusion and Contagion Processes on Networks

Empirical statistical analysis, visualization and simulation of diffusion and contagion processes on networks. The package implements algorithms for calculating network diffusion statistics such as transmission rate, hazard rates, exposure models, network threshold levels, infectiousness (contagion), and susceptibility. The package is inspired by work published in Valente, et al., (2015) <DOI:10.1016/j.socscimed.2015.10.001>; Valente (1995) <ISBN: 9781881303213>, Myers (2000) <DOI:10.1086/303110>, Iyengar and others (2011) <DOI:10.1287/mksc.1100.0566>, Burt (1987) <DOI:10.1086/228667>; among others.

Maintained by George Vega Yon. Last updated 4 months ago.

contagion diffusion-network network-analysis network-visualization openblas cpp openmp

4.9 match 88 stars 8.88 score 217 scripts

inlabru-org

fmesher:Triangle Meshes and Related Geometry Tools

Generate planar and spherical triangle meshes, compute finite element calculations for 1- and 2-dimensional flat and curved manifolds with associated basis function spaces, methods for lines and polygons, and transparent handling of coordinate reference systems and coordinate transformation, including 'sf' and 'sp' geometries. The core 'fmesher' library code was originally part of the 'INLA' package, and implements parts of "Triangulations and Applications" by Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.

Maintained by Finn Lindgren. Last updated 16 hours ago.

cpp

3.8 match 16 stars 11.28 score 261 scripts 26 dependents

paulnorthrop

donut:Nearest Neighbour Search with Variables on a Torus

Finds the k nearest neighbours in a dataset of specified points, adding the option to wrap certain variables on a torus. The user chooses the algorithm to use to find the nearest neighbours. Two such algorithms, provided by the packages 'RANN' <https://cran.r-project.org/package=RANN>, and 'nabor' <https://cran.r-project.org/package=nabor>, are suggested.

Maintained by Paul J. Northrop. Last updated 2 years ago.

degrees donut edges knn-algorithm knn-search nabor nearest nearest-neighbor nearest-neighbor-search nearest-neighbors nearest-neighbour-algorithm nearest-neighbours neighbors periodicity rann torus wrap

10.0 match 1 stars 4.18 score 5 scripts 1 dependents

mbeauvai

AFM:Atomic Force Microscope Image Analysis

Provides Atomic Force Microscope images analysis such as Gaussian mixes identification, Power Spectral Density, roughness against lengthscale, experimental variogram and variogram models, fractal dimension and scale, 2D network analysis. The AFM images can be exported to STL format for 3D printing.

Maintained by Mathieu Beauvais. Last updated 4 years ago.

14.1 match 1 stars 2.96 score 92 scripts

taxonomicallyinformedannotation

tima:Taxonomically Informed Metabolite Annotation

This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.

Maintained by Adriano Rutz. Last updated 15 hours ago.

metabolite annotation chemotaxonomy scoring system natural products computational metabolomics taxonomic distance specialized metabolome

6.3 match 9 stars 6.56 score 32 scripts 2 dependents

ropensci

rix:Reproducible Data Science Environments with 'Nix'

Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.

Maintained by Bruno Rodrigues. Last updated 11 hours ago.

nix peer-reviewed reproducibility reproducible-research

3.9 match 239 stars 10.56 score 67 scripts

annennenne

causalDisco:Tools for Causal Discovery on Observational Data

Various tools for inferring causal models from observational data. The package includes an implementation of the temporal Peter-Clark (TPC) algorithm. Petersen, Osler and Ekstrøm (2021) <doi:10.1093/aje/kwab087>. It also includes general tools for evaluating differences in adjacency matrices, which can be used for evaluating performance of causal discovery procedures.

Maintained by Anne Helby Petersen. Last updated 29 days ago.

8.6 match 19 stars 4.76 score 10 scripts

agoutsmedt

biblionetwork:Create Different Types of Bibliometric Networks

Functions to find edges for bibliometric networks like bibliographic coupling network, co-citation network and co-authorship network. The weights of network edges can be calculated according to different methods, depending on the type of networks, the type of nodes, and what you want to analyse. These functions are optimized to be be used on large dataset. The package contains functions inspired by: Leydesdorff, Loet and Park, Han Woo (2017) <doi:10.1016/j.joi.2016.11.007>; Perianes-Rodriguez, Antonio, Ludo Waltman, and Nees Jan Van Eck (2016) <doi:10.1016/j.joi.2016.10.006>; Sen, Subir K. and Shymal K. Gan (1983) <http://nopr.niscair.res.in/handle/123456789/28008>; Shen, Si, Zhu, Danhao, Rousseau, Ronald, Su, Xinning and Wang, Dongbo (2019) <doi:10.1016/j.joi.2019.01.012>; Zhao, Dangzhi and Strotmann, Andreas (2008) <doi:10.1002/meet.2008.1450450292>.

Maintained by Aurélien Goutsmedt. Last updated 2 years ago.

authorship-network bibliometric-networks bibliometrics coupling-angle

7.9 match 7 stars 5.18 score 43 scripts

chiliubio

meconetcomp:Compare Microbial Networks of 'trans_network' Class of 'microeco' Package

Compare microbial co-occurrence networks created from 'trans_network' class of 'microeco' package <https://github.com/ChiLiubio/microeco>. This package is the extension of 'trans_network' class of 'microeco' package and especially useful when different networks are constructed and analyzed simultaneously.

Maintained by Chi Liu. Last updated 1 months ago.

8.6 match 10 stars 4.73 score 12 scripts

yihui

knitr:A General-Purpose Package for Dynamic Report Generation in R

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

Maintained by Yihui Xie. Last updated 15 hours ago.

dynamic-documents knitr literate-programming rmarkdown sweave

1.7 match 2.4k stars 23.64 score 116k scripts 4.2k dependents

bioc

SplicingGraphs:Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.

Maintained by H. Pagès. Last updated 5 months ago.

genetics annotation datarepresentation visualization sequencing rnaseq geneexpression alternativesplicing transcription immunooncology bioconductor-package

7.7 match 2 stars 5.26 score 8 scripts

cran

rcausim:Generate Causally-Simulated Data

Generate causally-simulated data to serve as ground truth for evaluating methods in causal discovery and effect estimation. The package provides tools to assist in defining functions based on specified edges, and conversely, defining edges based on functions. It enables the generation of data according to these predefined functions and causal structures. This is particularly useful for researchers in fields such as artificial intelligence, statistics, biology, medicine, epidemiology, economics, and social sciences, who are developing a general or a domain-specific methods to discover causal structures and estimate causal effects. Data simulation adheres to principles of structural causal modeling. Detailed methodologies and examples are documented in our vignette, available at <https://htmlpreview.github.io/?https://github.com/herdiantrisufriyana/rcausim/blob/master/doc/causal_simulation_exemplar.html>.

Maintained by Herdiantri Sufriyana. Last updated 9 months ago.

13.4 match 3.00 score

jonnob

rsetse:Strain Elevation Tension Spring Embedding

An R implementation for the Strain Elevation and Tension embedding algorithm from Bourne (2020) <doi:10.1007/s41109-020-00329-4>. The package embeds graphs and networks using the Strain Elevation and Tension embedding (SETSe) algorithm. SETSe represents the network as a physical system, where edges are elastic, and nodes exert a force either up or down based on node features. SETSe positions the nodes vertically such that the tension in the edges of a node is equal and opposite to the force it exerts for all nodes in the network. The resultant structure can then be analysed by looking at the node elevation and the edge strain and tension. This algorithm works on weighted and unweighted networks as well as networks with or without explicit node features. Edge elasticity can be created from existing edge weights or kept as a constant.

Maintained by Jonathan Bourne. Last updated 3 years ago.

embedding embedding-graphs graph-embedding igraph networks networkscience unsupervised-learning openblas cpp openmp

8.2 match 7 stars 4.85 score 8 scripts

pbastide

PhylogeneticEM:Automatic Shift Detection using a Phylogenetic EM

Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on phylogenies. Some tools to handle equivalent shifts configurations are also available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.

Maintained by Paul Bastide. Last updated 2 months ago.

openblas cpp

5.8 match 17 stars 6.81 score 47 scripts

bioc

Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.

Maintained by Nan Xiao. Last updated 5 months ago.

software dataimport datarepresentation featureextraction cheminformatics biomedicalinformatics proteomics go systemsbiology bioconductor bioinformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

5.0 match 37 stars 7.81 score 29 scripts

gi0na

ghypernet:Fit and Simulate Generalised Hypergeometric Ensembles of Graphs

Provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG). To learn how to use it, check the vignettes for a quick tutorial. Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300> together with those relevant references from the one listed below. The package is based on the research developed at the Chair of Systems Design, ETH Zurich. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arXiv:1607.02441>. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>. Casiraghi, G., (2017) <arXiv:1702.02048> Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926> Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>. Casiraghi, G., Nanumyan, V. (2021) <doi:10.1038/s41598-021-92519-y>. Casiraghi, G. (2021) <doi:10.1088/2632-072X/ac0493>.

Maintained by Giona Casiraghi. Last updated 12 months ago.

data-mining data-science graphs network network-analysis random-graph-generation random-graphs

6.9 match 8 stars 5.68 score 20 scripts

thomaschln

sgraph:Network Visualization Using 'sigma.js'

Interactive visualizations of graphs created with the 'igraph' package using a 'htmlwidgets' wrapper for the 'sigma.js' network visualization v2.4.0 <https://www.sigmajs.org/>, enabling to display several thousands of nodes. While several 'R' packages have been developed to interface 'sigma.js', all were developed for v1.x.x and none have migrated to v2.4.0 nor are they planning to. This package builds upon the 'sigmaNet' package, and users familiar with it will recognize the similar design approach. Two extensions have been added to the classic 'sigma.js' visualizations by overriding the underlying 'JavaScript' code, enabling to draw a frame around node labels, and to display labels on multiple lines by parsing line breaks. Other additional functionalities that did not require overriding 'sigma.js' code include toggling node visibility when clicked using a node attribute and highlighting specific edges. 'sigma.js' is currently preparing a stable release v3.0.0, and this package plans to update to it when it is available.

Maintained by Thomas Charlon. Last updated 4 months ago.

7.7 match 5.02 score 1 scripts 1 dependents

hypertidy

silicate:Common Forms for Complex Hierarchical and Relational Data Structures

Generate common data forms for complex data suitable for conversions and transmission by decomposition as paths or primitives. Paths are sequentially-linked records, primitives are basic atomic elements and both can model many forms and be grouped into hierarchical structures. The universal models 'SC0' (structural) and 'SC' (labelled, relational) are composed of edges and can represent any hierarchical form. Specialist models 'PATH', 'ARC' and 'TRI' provide the most common intermediate forms used for converting from one form to another. The methods are inspired by the simplicial complex <https://en.wikipedia.org/wiki/Simplicial_complex> and provide intermediate forms that relate spatial data structures to this mathematical construct.

Maintained by Michael D. Sumner. Last updated 1 years ago.

hierarchical-data simplicial-complex spatial-data structural-primitives topology triangulation

5.3 match 54 stars 7.28 score 111 scripts 7 dependents

stla

cxhull:Convex Hull

Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.

Maintained by Stéphane Laurent. Last updated 1 years ago.

computational-geometry convex-hull

6.4 match 14 stars 5.93 score 81 scripts 5 dependents

dwbapst

paleotree:Paleontological and Phylogenetic Analyses of Evolution

Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.

Maintained by David W. Bapst. Last updated 9 months ago.

5.1 match 21 stars 7.53 score 216 scripts 2 dependents

billpetti

baseballr:Acquiring and Analyzing Baseball Data

Provides numerous utilities for acquiring and analyzing baseball data from online sources such as 'Baseball Reference' <https://www.baseball-reference.com/>, 'FanGraphs' <https://www.fangraphs.com/>, and the 'MLB Stats' API <https://www.mlb.com/>.

Maintained by Saiem Gilani. Last updated 5 months ago.

baseball pitchfx sabermetrics statcast

4.3 match 380 stars 8.98 score 582 scripts

venelin

PCMBase:Simulation and Likelihood Calculation of Phylogenetic Comparative Models

Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for inference of these models to tree and trait data. The package web-site <https://venelin.github.io/PCMBase/> provides access to the documentation and other resources.

Maintained by Venelin Mitov. Last updated 11 months ago.

5.2 match 6 stars 7.26 score 85 scripts 3 dependents

ggobi

tourr:Tour Methods for Multivariate Data Visualisation

Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.

Maintained by Dianne Cook. Last updated 1 months ago.

3.3 match 65 stars 11.18 score 426 scripts 10 dependents

antiphon

spatgraphs:Graph Edge Computations for Spatial Point Patterns

Graphs (or networks) and graph component calculations for spatial locations in 1D, 2D, 3D etc.

Maintained by Tuomas Rajala. Last updated 11 months ago.

cpp

13.0 match 2 stars 2.81 score 16 scripts

stla

tessellation:Delaunay and Voronoï Tessellations

Delaunay and Voronoï tessellations, with emphasis on the two-dimensional and the three-dimensional cases (the package provides functions to plot the tessellations for these cases). Delaunay tessellations are computed in C with the help of the 'Qhull' library <http://www.qhull.org/>.

Maintained by Stéphane Laurent. Last updated 1 years ago.

c delaunay-triangulation voronoi-tessellation

6.9 match 17 stars 5.23 score 67 scripts 1 dependents

alishinski

lavaanPlot:Path Diagrams for 'Lavaan' Models via 'DiagrammeR'

Plots path diagrams from models in 'lavaan' using the plotting functionality from the 'DiagrammeR' package. 'DiagrammeR' provides nice path diagrams via 'Graphviz', and these functions make it easy to generate these diagrams from a 'lavaan' path model without having to write the DOT language graph specification.

Maintained by Alex Lishinski. Last updated 1 years ago.

4.3 match 40 stars 8.33 score 294 scripts

stathin

ggm:Graphical Markov Models with Mixed Graphs

Provides functions for defining mixed graphs containing three types of edges, directed, undirected and bi-directed, with possibly multiple edges. These graphs are useful because they capture fundamental independence structures in multivariate distributions and in the induced distributions after marginalization and conditioning. The package is especially concerned with Gaussian graphical models for (i) ML estimation for directed acyclic graphs, undirected and bi-directed graphs and ancestral graph models (ii) testing several conditional independencies (iii) checking global identification of DAG Gaussian models with one latent variable (iv) testing Markov equivalences and generating Markov equivalent graphs of specific types.

Maintained by Giovanni M. Marchetti. Last updated 1 years ago.

5.0 match 7.11 score 295 scripts 29 dependents

jmanuelmk

CoNI:Correlation Guided Network Integration (CoNI)

Integrates two numerical omics data sets from the same samples using partial correlations. The output can be represented as a network, bipartite graph or a hypergraph structure. The method used in the package refers to Klaus et al (2021) <doi:10.1016/j.molmet.2021.101295>.

Maintained by José Manuel Monroy Kuhn. Last updated 3 years ago.

9.6 match 3.70 score 2 scripts

bioc

rBiopaxParser:Parses BioPax files and represents them in R

Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.

Maintained by Frank Kramer. Last updated 5 months ago.

datarepresentation

6.1 match 10 stars 5.85 score 7 scripts

bnosac

image.libfacedetection:Convolutional Neural Network for Face Detection

An open source library for face detection in images. Provides a pretrained convolutional neural network based on <https://github.com/ShiqiYu/libfacedetection> which can be used to detect faces which have size greater than 10x10 pixels.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp openmp

6.7 match 279 stars 5.29 score 14 scripts

rspatial

terra:Spatial Data Analysis

Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).

Maintained by Robert J. Hijmans. Last updated 2 hours ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

2.0 match 560 stars 17.62 score 17k scripts 857 dependents

sinnweja

regmed:Regularized Mediation Analysis

Mediation analysis for multiple mediators by penalized structural equation models with different types of penalties depending on whether there are multiple mediators and only one exposure and one outcome variable (using sparse group lasso) or multiple exposures, multiple mediators, and multiple outcome variables (using lasso, L1, penalties).

Maintained by Jason Sinnwell. Last updated 2 years ago.

openblas cpp

11.7 match 2 stars 3.00 score 5 scripts

natverse

nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data

NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).

Maintained by Gregory Jefferis. Last updated 6 months ago.

3d connectomics image-analysis neuroanatomy neuroanatomy-toolbox neuron neuron-morphology neuroscience visualisation

3.5 match 67 stars 9.94 score 436 scripts 2 dependents

ropensci

magick:Advanced Graphics and Image-Processing in R

Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.

Maintained by Jeroen Ooms. Last updated 9 days ago.

image-manipulation image-processing imagemagick cpp

2.0 match 467 stars 17.38 score 9.0k scripts 258 dependents

rspatial

raster:Geographic Data Analysis and Modeling

Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.

Maintained by Robert J. Hijmans. Last updated 4 days ago.

cpp

2.0 match 163 stars 17.23 score 58k scripts 562 dependents

termehs

multigraphr:Probability Models and Statistical Analysis of Random Multigraphs

Methods and models for analysing multigraphs as introduced by Shafie (2015) <doi:10.21307/joss-2019-011>, including methods to study local and global properties <doi:10.1080/0022250X.2016.1219732> and goodness of fit tests.

Maintained by Termeh Shafie. Last updated 1 years ago.

6.4 match 16 stars 5.38 score 1 scripts

bnosac

image.Otsu:Otsu's Image Segmentation Method

An implementation of the Otsu's Image Segmentation Method described in the paper: "A C++ Implementation of Otsu's Image Segmentation Method". The algorithm is explained at <doi:10.5201/ipol.2016.158>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

6.7 match 279 stars 5.14 score

bnosac

image.CornerDetectionHarris:Implementation of the Harris Corner Detection for Images

An implementation of the Harris Corner Detection as described in the paper "An Analysis and Implementation of the Harris Corner Detector" by Sánchez J. et al (2018) available at <doi:10.5201/ipol.2018.229>. The package allows to detect relevant points in images which are characteristic to the digital image.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp openmp

6.7 match 279 stars 5.14 score 2 scripts

bnosac

image.CornerDetectionF9:Find Corners in Digital Images with FAST-9

An implementation of the "FAST-9" corner detection algorithm explained in the paper 'FASTER and better: A machine learning approach to corner detection' by Rosten E., Porter R. and Drummond T. (2008), available at <arXiv:0810.2434>. The package allows to detect corners in digital images.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

6.7 match 279 stars 5.14 score 7 scripts

bnosac

image.ContourDetector:Implementation of the Unsupervised Smooth Contour Line Detection for Images

An implementation of the Unsupervised Smooth Contour Detection algorithm for digital images as described in the paper: "Unsupervised Smooth Contour Detection" by Rafael Grompone von Gioi, and Gregory Randall (2016). The algorithm is explained at <doi:10.5201/ipol.2016.175>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

6.7 match 279 stars 5.14 score 7 scripts

bnosac

image.LineSegmentDetector:Detect Line Segments in Images

An implementation of the Line Segment Detector on digital images described in the paper: "LSD: A Fast Line Segment Detector with a False Detection Control" by Rafael Grompone von Gioi et al (2012). The algorithm is explained at <doi:10.5201/ipol.2012.gjmr-lsd>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

6.7 match 279 stars 5.14 score 7 scripts

pik-piam

mrtransport:Input data generation for the EDGE-Transport model

The mrtransport package contains data preprocessing for the EDGE-Transport model.

Maintained by Johanna Hoppe. Last updated 4 days ago.

7.0 match 4.86 score 3 dependents

cogbrainhealthlab

VertexWiseR:Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal Surface

Provides functions to run statistical analyses on surface-based neuroimaging data, computing measures including cortical thickness and surface area of the whole-brain and of the hippocampi. It can make use of 'FreeSurfer', 'fMRIprep', 'HCP' and 'CAT12' preprocessed datasets and 'HippUnfold' hippocampal segmentation outputs for a given sample by restructuring the data values into a single file. The single file can then be used by the package for analyses independently from its base dataset and without need for its access.

Maintained by Charly Billaud. Last updated 6 days ago.

5.8 match 1 stars 5.86 score 12 scripts

nanxstats

protr:Generating Various Numerical Representation Schemes for Protein Sequences

Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html> for more information.

Maintained by Nan Xiao. Last updated 7 months ago.

bioinformatics feature-engineering feature-extraction machine-learning peptides protein-sequences sequence-analysis

3.3 match 52 stars 10.02 score 173 scripts 3 dependents

davidcsterratt

retistruct:Retinal Reconstruction Program

Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates. For more details see Sterratt, D. C., Lyngholm, D., Willshaw, D. J. and Thompson, I. D. (2013) <doi:10.1371/journal.pcbi.1002921>.

Maintained by David C. Sterratt. Last updated 4 days ago.

7.0 match 8 stars 4.75 score

bioc

TSCAN:Tools for Single-Cell Analysis

Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.

Maintained by Zhicheng Ji. Last updated 5 months ago.

geneexpression visualization gui

4.4 match 7.58 score 207 scripts 3 dependents

trinker

textshape:Tools for Reshaping Text

Tools that can be used to reshape and restructure text data.

Maintained by Tyler Rinker. Last updated 1 years ago.

data-reshaping manipulation sentence-boundary-detection text-data text-formating tidy

3.6 match 50 stars 9.18 score 266 scripts 34 dependents

pik-piam

reporttransport:Reporting package for edgeTransport

This package contains edgeTransport-specific routines to report model results. The main functionality is to generate transport reporting variables in MIF format from a given edgeTransport model run folder or REMIND input data.

Maintained by Johanna Hoppe. Last updated 2 months ago.

7.2 match 4.60 score 9 scripts 3 dependents

sebastien-plutniak

archeofrag:Spatial Analysis in Archaeology from Refitting Fragments

Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. Empirical datasets are provided as examples. Documentation about 'archeofrag' is provided by the vignette included in this package, by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by a companion GUI application available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.

Maintained by Sebastien Plutniak. Last updated 5 days ago.

archaeological-objects archaeological-science archaeology fragmentation network-analysis

5.1 match 20 stars 6.48 score 10 scripts 1 dependents

r-lib

gtable:Arrange 'Grobs' in Tables

Tools to make it easier to work with "tables" of 'grobs'. The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.

Maintained by Thomas Lin Pedersen. Last updated 5 months ago.

1.8 match 92 stars 18.12 score 4.1k scripts 7.6k dependents

modesto-escobar

netCoin:Interactive Analytic Networks

Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.

Maintained by Modesto Escobar. Last updated 4 days ago.

4.5 match 11 stars 7.22 score 47 scripts

jayanilakshika

quollr:Visualising How Nonlinear Dimension Reduction Warps Your Data

To construct a model in 2D space from 2D embedding data and then lift it to the high-dimensional space. Additionally, it provides tools to visualize the model in 2D space and to overlay the fitted model on data using the tour technique. Furthermore, it facilitates the generation of summaries of high-dimensional distributions.

Maintained by Jayani P.G. Lakshika. Last updated 2 days ago.

7.3 match 3 stars 4.48 score 7 scripts

pet221

SSNbler:Assemble 'SSN' Objects

Import, create and assemble data needed to fit spatial-statistical stream-network models using the 'SSN2' package for 'R'. Streams, observations, and prediction locations are represented as simple features and specific tools provided to define topological relationships between features; calculate the hydrologic distances (with flow-direction preserved) and the spatial additive function used to weight converging stream segments; and export the topological, spatial, and attribute information to an `SSN` (spatial stream network) object, which can be efficiently stored, accessed and analysed in 'R'. A detailed description of methods used to calculate and format the spatial data can be found in Peterson, E.E. and Ver Hoef, J.M., (2014) <doi:10.18637/jss.v056.i02>.

Maintained by Erin Peterson. Last updated 6 days ago.

5.3 match 10 stars 6.04 score 17 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-quality health-informatics semantic-enrichment

6.5 match 8 stars 4.90 score 10 scripts

johncoene

graphTweets:Visualise Twitter Interactions

Allows building an edge table from data frame of tweets, also provides function to build nodes and another create a temporal graph.

Maintained by John Coene. Last updated 5 years ago.

network-analysis twitter

5.8 match 46 stars 5.49 score 67 scripts

jafarilab

NIMAA:Nominal Data Mining Analysis

Functions for nominal data mining based on bipartite graphs, which build a pipeline for analysis and missing values imputation. Methods are mainly from the paper: Jafari, Mohieddin, et al. (2021) <doi:10.1101/2021.03.18.436040>, some new ones are also included.

Maintained by Mohieddin Jafari. Last updated 2 years ago.

7.3 match 4 stars 4.30 score 7 scripts

statnet

latentnet:Latent Position and Cluster Models for Statistical Networks

Fit and simulate latent position and cluster models for statistical networks. See Krivitsky and Handcock (2008) <doi:10.18637/jss.v024.i05> and Krivitsky, Handcock, Raftery, and Hoff (2009) <doi:10.1016/j.socnet.2009.04.001>.

Maintained by Pavel N. Krivitsky. Last updated 21 days ago.

openblas

3.8 match 19 stars 8.36 score 191 scripts 4 dependents

asa12138

MetaNet:Network Analysis for Omics Data

Comprehensive network analysis package. Calculate correlation network fastly, accelerate lots of analysis by parallel computing. Support for multi-omics data, search sub-nets fluently. Handle bigger data, more than 10,000 nodes in each omics. Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize. Provide comprehensive topology indexes calculation, including ecological network stability.

Maintained by Chen Peng. Last updated 13 days ago.

dataimport network analysis omics software visualization

5.6 match 13 stars 5.59 score 9 scripts

squidlobster

castor:Efficient Phylogenetics on Large Trees

Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.

Maintained by Stilianos Louca. Last updated 4 months ago.

cpp

5.4 match 2 stars 5.75 score 450 scripts 9 dependents

uclahs-cds

CancerEvolutionVisualization:Publication Quality Phylogenetic Tree Plots

Generates tree plots with precise branch lengths, gene annotations, and cellular prevalence. The package handles complex tree structures (angles, lengths, etc.) and can be further refined as needed by the user.

Maintained by Paul Boutros. Last updated 14 days ago.

4.8 match 2 stars 6.44 score 5 scripts

bioc

graphite:GRAPH Interaction from pathway Topological Environment

Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.

Maintained by Gabriele Sales. Last updated 5 months ago.

pathways thirdpartyclient graphandnetwork network reactome kegg metabolomics bioinformatics mirror pathway-analysis

3.0 match 8 stars 10.24 score 122 scripts 21 dependents

bips-hb

CVN:Covariate-Varying Networks

Inferring high-dimensional Gaussian graphical networks that change with multiple discrete covariates. Louis Dijkstra, Arne Godt, Ronja Foraita (2024) <doi:10.48550/arXiv.2407.19978>.

Maintained by Ronja Foraita. Last updated 14 hours ago.

graphical-models high-dimensional-statistics network-analysis cpp

8.1 match 3.78 score 7 scripts

mathewchamberlain

SignacX:Cell Type Identification and Discovery from Single Cell Gene Expression Data

An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) <doi:10.1101/2021.02.01.429207> for more details.

Maintained by Mathew Chamberlain. Last updated 2 years ago.

cellular-phenotypes seurat single-cell-rna-seq

4.7 match 25 stars 6.47 score 34 scripts

bodkan

slendr:A Simulation Framework for Spatiotemporal Population Genetics

A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.

Maintained by Martin Petr. Last updated 3 days ago.

popgen population-genetics simulations spatial-statistics

3.3 match 56 stars 9.13 score 88 scripts

darunabas

phyloregion:Biogeographic Regionalization and Macroecology

Computational infrastructure for biogeography, community ecology, and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>. It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>. The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013> on patterns and processes of biogeographical regionalization. Additionally, the package contains fast and efficient functions to compute more standard conservation measures such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and global endangerment, as well as compositional turnover (e.g., beta diversity).

Maintained by Barnabas H. Daru. Last updated 5 months ago.

software

4.2 match 18 stars 7.21 score 50 scripts 1 dependents

csprock

Rwclust:Random Walk Clustering on Weighted Graphs

Implements the random walk clustering algorithm for weighted graphs as found in Harel and Koren (2001) <https://link.springer.com/chapter/10.1007/3-540-45294-X_3>.

Maintained by Carson Sprock. Last updated 3 years ago.

8.0 match 1 stars 3.70 score 4 scripts

eguidotti

bidask:Efficient Estimation of Bid-Ask Spreads from Open, High, Low, and Close Prices

Implements the efficient estimator of bid-ask spreads from open, high, low, and close prices described in Ardia, Guidotti, & Kroencke (JFE, 2024) <doi:10.1016/j.jfineco.2024.103916>. It also provides an implementation of the estimators described in Roll (JF, 1984) <doi:10.1111/j.1540-6261.1984.tb03897.x>, Corwin & Schultz (JF, 2012) <doi:10.1111/j.1540-6261.2012.01729.x>, and Abdi & Ranaldo (RFS, 2017) <doi:10.1093/rfs/hhx084>.

Maintained by Emanuele Guidotti. Last updated 1 months ago.

finance

4.3 match 109 stars 6.99 score 6 scripts

bioc

RBGL:An interface to the BOOST graph library

A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

graphandnetwork network cpp

3.4 match 8.59 score 320 scripts 132 dependents

ropensci

rOPTRAM:Derive Soil Moisture Using the OPTRAM Algorithm

The OPtical TRapezoid Model (OPTRAM) derives soil moisture based on the linear relation between a vegetation index and Land Surface Temperature (LST). The Short Wave Infra-red (SWIR) band is used as a proxy for LST. See: Sadeghi, M. et al., 2017. <https://doi.org/10.1016/j.rse.2017.05.041> .

Maintained by Micha Silver. Last updated 2 months ago.

5.1 match 9 stars 5.73 score 6 scripts

spaceodyssey

cia:Learn and Apply Directed Acyclic Graphs for Causal Inference

Causal Inference Assistance (CIA) for performing causal inference within the structural causal modelling framework. Structure learning is performed using partition Markov chain Monte Carlo (Kuipers & Moffa, 2017) and several additional functions have been added to help with causal inference. Kuipers and Moffa (2017) <doi:10.1080/01621459.2015.1133426>.

Maintained by Mathew Varidel. Last updated 3 months ago.

7.6 match 3.85 score 5 scripts

nepem-ufsc

pliman:Tools for Plant Image Analysis

Tools for both single and batch image manipulation and analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>). The tools can be used for the quantification of leaf area, object counting, extraction of image indexes, shape measurement, object landmark identification, and Elliptical Fourier Analysis of object outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package also provides a comprehensive pipeline for generating shapefiles with complex layouts and supports high-throughput phenotyping of RGB, multispectral, and hyperspectral orthomosaics. This functionality facilitates field phenotyping using UAV- or satellite-based imagery.

Maintained by Tiago Olivoto. Last updated 4 days ago.

openblas fftw3 cpp openmp

4.3 match 11 stars 6.76 score 476 scripts

bioc

BioQC:Detect tissue heterogeneity in expression profiles with gene sets

BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.

Maintained by Jitao David Zhang. Last updated 5 months ago.

geneexpression qualitycontrol statisticalmethod genesetenrichment cpp

3.5 match 5 stars 8.16 score 86 scripts

welch-lab

cytosignal:What the Package Does (One Line, Title Case)

What the package does (one paragraph).

Maintained by Jialin Liu. Last updated 11 hours ago.

openblas cpp

4.6 match 17 stars 6.11 score 6 scripts

guenardg

MPSEM:Modelling Phylogenetic Signals using Eigenvector Maps

Computational tools to represent phylogenetic signals using adapted eigenvector maps.

Maintained by Guillaume Guénard. Last updated 7 months ago.

5.8 match 4.80 score 21 scripts 1 dependents

r-forge

pcalg:Methods for Graphical Models and Causal Inference

Functions for causal structure learning and causal inference using graphical models. The main algorithms for causal structure learning are PC (for observational data without hidden variables), FCI and RFCI (for observational data with hidden variables), and GIES (for a mix of data from observational studies (i.e. observational data) and data from experiments involving interventions (i.e. interventional data) without hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some related functions are implemented. Functions for incorporating background knowledge are provided.

Maintained by Markus Kalisch. Last updated 7 months ago.

openblas cpp

3.8 match 7.30 score 700 scripts 19 dependents

krisrs1128

multimedia:Multimodal Mediation Analysis

Multimodal mediation analysis is an emerging problem in microbiome data analysis. Multimedia make advanced mediation analysis techniques easy to use, ensuring that all statistical components are transparent and adaptable to specific problem contexts. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, bootstrap confidence interval construction, and sensitivity analysis. More details are available in Jiang et al. (2024) "multimedia: Multimodal Mediation Analysis of Microbiome Data" <doi:10.1101/2024.03.27.587024>.

Maintained by Kris Sankaran. Last updated 2 months ago.

coverage microbiome regression sequencing software statisticalmethod structuralequationmodels causal-inference data-integration mediation-analysis

5.0 match 1 stars 5.49 score 13 scripts

petergreen5678

gRaven:Bayes Nets: 'RHugin' Emulation with 'gRain'

Wrappers for functions in the 'gRain' package to emulate some 'RHugin' functionality, allowing the building of Bayesian networks consisting on discrete chance nodes incrementally, through adding nodes, edges and conditional probability tables, the setting of evidence, both 'hard' (boolean) or 'soft' (likelihoods), querying marginal probabilities and normalizing constants, and generating sets of high-probability configurations. Computations will typically not be so fast as they are with 'RHugin', but this package should assist users without access to 'Hugin' to use code written to use 'RHugin'.

Maintained by Peter Green. Last updated 6 months ago.

10.8 match 2.48 score 2 scripts 2 dependents

guangchuangyu

ggtangle:Draw Network with Data

Extends the 'ggplot2' plotting system to support network visualization. Inspired by the 'Method 1' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'ggtangle' is designed to work with network associated data.

Maintained by Guangchuang Yu. Last updated 3 months ago.

3.9 match 1 stars 6.87 score 3 scripts 59 dependents

ropensci

targets:Dynamic Function-Oriented 'Make'-Like Declarative Pipelines

Pipeline tools coordinate the pieces of computationally demanding analysis projects. The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).

Maintained by William Michael Landau. Last updated 4 hours ago.

data-science high-performance-computing make peer-reviewed pipeline r-targetopia reproducibility reproducible-research targets workflow

1.8 match 979 stars 15.15 score 4.6k scripts 22 dependents

dynverse

dynwrap:Representing and Inferring Single-Cell Trajectories

Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

trajectory-inference

3.5 match 16 stars 7.48 score 159 scripts 1 dependents

josiahparry

sfdep:Spatial Dependence for Simple Features

An interface to 'spdep' to integrate with 'sf' objects and the 'tidyverse'.

Maintained by Dexter Locke. Last updated 7 months ago.

r-spatial spatial

3.8 match 130 stars 7.01 score 130 scripts

dfsp-spirit

fsbrain:Managing and Visualizing Brain Surface Data

Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.

Maintained by Tim Schäfer. Last updated 4 months ago.

3d brain dti freesurfer mesh mri neuroimaging research surface visualization voxel

4.0 match 68 stars 6.49 score 15 scripts

usccana

netplot:Beautiful Graph Drawing

A graph visualization engine that emphasizes on aesthetics at the same time providing default parameters that yield out-of-the-box-nice visualizations. The package is built on top of 'The Grid Graphics Package' and seamlessly work with 'igraph' and 'network' objects.

Maintained by George Vega Yon. Last updated 5 months ago.

graph-visualization igraph netsci network-analysis network-visualization sna statnet

3.8 match 51 stars 6.90 score 78 scripts

january3

tmod:Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Methods and feature set definitions for feature or gene set enrichment analysis in transcriptional and metabolic profiling data. Package includes tests for enrichment based on ranked lists of features, functions for visualisation and multivariate functional analysis. See Zyla et al (2019) <doi:10.1093/bioinformatics/btz447>.

Maintained by January Weiner. Last updated 2 months ago.

3.8 match 3 stars 6.88 score 168 scripts 1 dependents

hedgehogqa

hedgehog:Property-Based Testing

Hedgehog will eat all your bugs. 'Hedgehog' is a property-based testing package in the spirit of 'QuickCheck'. With 'Hedgehog', one can test properties of their programs against randomly generated input, providing far superior test coverage compared to unit testing. One of the key benefits of 'Hedgehog' is integrated shrinking of counterexamples, which allows one to quickly find the cause of bugs, given salient examples when incorrect behaviour occurs.

Maintained by Huw Campbell. Last updated 4 years ago.

3.5 match 56 stars 7.33 score 63 scripts 1 dependents

kharchenkolab

pagoda2:Single Cell Analysis and Differential Expression

Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.

Maintained by Evan Biederstedt. Last updated 1 years ago.

scrna-seq single-cell single-cell-rna-seq transcriptomics openblas cpp openmp

3.2 match 223 stars 8.00 score 282 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.

edges igraph sc-form

10.0 match 7 stars 2.54 score 10 scripts

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.

4.7 match 15 stars 5.43 score 18 scripts

cran

GeneNet:Modeling and Inferring Gene Networks

Analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).

Maintained by Korbinian Strimmer. Last updated 3 years ago.

8.0 match 3.18 score 5 dependents

cran

sna:Tools for Social Network Analysis

A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.

Maintained by Carter T. Butts. Last updated 7 months ago.

3.7 match 8 stars 6.78 score 94 dependents

ogarciav

siplab:Spatial Individual-Plant Modelling

A platform for computing competition indices and experimenting with spatially explicit individual-based vegetation models.

Maintained by Oscar Garcia. Last updated 3 years ago.

plant-ecology plant-growth simulation

5.0 match 3 stars 4.97 score 31 scripts

davidcsterratt

geometry:Mesh Generation and Surface Tessellation

Makes the 'Qhull' library <http://www.qhull.org> available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this.

Maintained by David C. Sterratt. Last updated 2 months ago.

cpp

1.9 match 16 stars 12.98 score 776 scripts 139 dependents

alarm-redist

redistmetrics:Redistricting Metrics

Reliable and flexible tools for scoring redistricting plans using common measures and metrics. These functions provide key direct access to tools useful for non-simulation analyses of redistricting plans, such as for measuring compactness or partisan fairness. Tools are designed to work with the 'redist' package seamlessly.

Maintained by Christopher T. Kenny. Last updated 10 months ago.

openblas cpp

3.2 match 10 stars 7.57 score 23 scripts 2 dependents

kasperwelbers

RNewsflow:Tools for Comparing Text Messages Across Time and Media

A collection of tools for measuring the similarity of text messages and tracing the flow of messages over time and across media.

Maintained by Kasper Welbers. Last updated 12 months ago.

cpp

3.5 match 37 stars 6.93 score 31 scripts 2 dependents

bjoelle

FossilSim:Simulation and Plots for Fossil and Taxonomy Data

Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.

Maintained by Joelle Barido-Sottani. Last updated 6 months ago.

4.6 match 1 stars 5.24 score 65 scripts 1 dependents

bioc

SPONGE:Sparse Partial Correlations On Gene Expression

This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

Maintained by Markus List. Last updated 5 months ago.

geneexpression transcription generegulation networkinference transcriptomics systemsbiology regression randomforest machinelearning

3.6 match 6.66 score 38 scripts 1 dependents

landscitech

roads:Road Network Projection

Iterative least cost path and minimum spanning tree methods for projecting forest road networks. The methods connect a set of target points to an existing road network using 'igraph' <https://igraph.org> to identify least cost routes. The cost of constructing a road segment between adjacent pixels is determined by a user supplied weight raster and a weight function; options include the average of adjacent weight raster values, and a function of the elevation differences between adjacent cells that penalizes steep grades. These road network projection methods are intended for integration into R workflows and modelling frameworks used for forecasting forest change, and can be applied over multiple time-steps without rebuilding a graph at each time-step.

Maintained by Sarah Endicott. Last updated 7 months ago.

3.6 match 4 stars 6.54 score 29 scripts

bioc

NetPathMiner:NetPathMiner for Biological Network Construction, Path Mining and Visualization

NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.

Maintained by Ahmed Mohamed. Last updated 4 months ago.

graphandnetwork pathways network clustering classification libsbml libxml2 openblas cpp

3.6 match 9 stars 6.56 score 9 scripts

flyaflya

causact:Fast, Easy, and Visual Bayesian Inference

Accelerate Bayesian analytics workflows in 'R' through interactive modelling, visualization, and inference. Define probabilistic graphical models using directed acyclic graphs (DAGs) as a unifying language for business stakeholders, statisticians, and programmers. This package relies on interfacing with the 'numpyro' python package.

Maintained by Adam Fleischhacker. Last updated 2 months ago.

bayesian-inference dags posterior-probability probabilistic-graphical-models probabilistic-programming

3.4 match 45 stars 6.97 score 52 scripts

cran

cyjShiny:Cytoscape.js Shiny Widget (cyjShiny)

Wraps cytoscape.js as a shiny widget. cytoscape.js <https://js.cytoscape.org/> is a Javascript-based graph theory (network) library for visualization and analysis. This package supports the visualization of networks with custom visual styles and several available layouts. Demo Shiny applications are provided in the package code.

Maintained by Augustin Luna. Last updated 2 years ago.

8.7 match 2.70 score

psavary3

graph4lg:Build Graphs for Landscape Genetics Analysis

Build graphs for landscape genetics analysis. This set of functions can be used to import and convert spatial and genetic data initially in different formats, import landscape graphs created with 'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>, make diagnosis plots of isolation by distance relationships in order to choose how to build genetic graphs, create graphs with a large range of pruning methods, weight their links with several genetic distances, plot and analyse graphs, compare them with other graphs. It uses functions from other packages such as 'adegenet' (Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi et Nepusz, 2006) <https://igraph.org/>. It also implements methods commonly used in landscape genetics to create graphs, described by Dyer et Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data (van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.

Maintained by Paul Savary. Last updated 2 years ago.

5.2 match 3 stars 4.51 score 54 scripts

bryanhanson

HiveR:2D and 3D Hive Plots for R

Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.

Maintained by Bryan A. Hanson. Last updated 9 months ago.

3.4 match 72 stars 6.76 score 53 scripts 2 dependents

thijsjanzen

nLTT:Calculate the NLTT Statistic

Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.

Maintained by Thijs Janzen. Last updated 2 years ago.

nltt nltt-statistic phylogenetic-trees phylogenetics

3.3 match 6 stars 6.93 score 59 scripts