
COVAIN
 Referenced in 1 article
[sw10556]
 combination of univariate and multivariate statistics, network topology and biochemical pathway mapping analysis ... multivariate statistical analysis, Granger timeseries analysis, pathway mapping, correlation network topology analysis and visualization...

ergm.graphlets
 Referenced in 4 articles
[sw20899]
 additional network statistics. Here, our focus is on the addition of statistics based on graphlets ... induced subgraphs that describe the topological structure of a network. We introduce an R package ... graphlet properties of a network within the ergm package of R. The ergm.graphlets package provides ... model terms that allows to incorporate statistics of any 2, 3, 4 and 5node...

QNet
 Referenced in 11 articles
[sw19662]
 Java which encompasses methods for generating phylogenetic networks from quartet data, as per the method ... topologies for a given data set, together with a branch length for each topology. These ... generating quartet weight data. GWeight utilizes statistical geometry [2] to generate quartet weights. LengthWeighter ... agglomerative approach to construct a planar split network, that summarises the relations described...

STARS
 Referenced in 3 articles
[sw24263]
 information needed to fit spatial statistical models to stream network data using the SSN package ... with a landscape network (LSN), which is a topological data model produced by the FLoWS...

ARTCP
 Referenced in 3 articles
[sw02294]
 principles, this model allows building simulation network topology of great complexity and setting various environments ... which ARTCP has over standard TCP algorithms. Statistical analysis of ARTCP traffic traces yields ... with other studies of traffic traces in network systems...

CytoNCA
 Referenced in 2 articles
[sw25624]
 edges in the network, to integrate biological data with topological data to detect specific nodes ... calculation results, and evaluate the accuracy by statistical measures. (v) Besides current eight centrality measures ... calculating centrality, evaluating and visualizing biological networks. AVAILABILITY: http://apps.cytoscape.org/apps/cytonca....

GRETNA
 Referenced in 1 article
[sw26509]
 statistics, toolboxes incorporating these functions are largely lacking. Here, we developed the GRaph thEoreTical Network ... interface (GUI); (ii) allowing topological analyses of global and local network properties with parallel computing ... during network construction and analysis, which include network node definition, network connectivity processing, network type ... choice of thresholding procedure; (iv) allowing statistical comparisons of global, nodal and connectional network metrics...

PrimAlign
 Referenced in 1 article
[sw34148]
 topology of PPIs between orthologs is often conserved. However, high accuracy and scalability of network ... Results: We propose a novel pairwise global network alignment algorithm, called PrimAlign, which is modeled ... networks. The experimental results demonstrate that PrimAlign outperforms several prevalent methods with statistically significant differences ... done with synthetic networks and results suggest that popular topological measures do not reflect real...

NATbox
 Referenced in 2 articles
[sw32087]
 opensource GUI implemented in the R statistical language for modelling and analysis ... given data (ii) model FRs and network structure from gene expression profiles using a battery ... acyclic graphs for visualization and investigate its topological properties using network analysis metrics, (iv) retrieve...

AlignNemo
 Referenced in 0 articles
[sw34159]
 each step explores the local topology of the networks beyond the proteins directly interacting with ... series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets...

ACL2
 Referenced in 277 articles
[sw00060]
 ACL2 is both a programming language in which...

BARON
 Referenced in 311 articles
[sw00066]
 BARON is a computational system for solving nonconvex...

CGAL
 Referenced in 355 articles
[sw00118]
 The goal of the CGAL Open Source Project...

CoCoA
 Referenced in 621 articles
[sw00143]
 CoCoA is a system for Computations in Commutative...

DRAGON
 Referenced in 15 articles
[sw00220]
 Dragon is an application for the calculation of...

GAP
 Referenced in 2850 articles
[sw00320]
 GAP is a system for computational discrete algebra...

InterViewer
 Referenced in 28 articles
[sw00443]
 InterViewer: Dynamic visualization of proteinprotein interactions From...

LAPACK
 Referenced in 1626 articles
[sw00503]
 LAPACK is written in Fortran 90 and provides...

LSQR
 Referenced in 358 articles
[sw00530]
 Algorithm 583: LSQR: Sparse Linear Equations and Least...

Macaulay2
 Referenced in 1658 articles
[sw00537]
 Macaulay2 is a software system devoted to supporting...