• Persistence Landscape

  • Referenced in 14 articles [sw21260]
  • persistence landscapes toolbox for topological statistics. Topological data analysis provides a multiscale description ... topological summary that can be easily combined with tools from statistics and machine learning ... facilitate the combination of statistics and machine learning with topological data analysis. We present...
  • TDA

  • Referenced in 17 articles [sw15508]
  • package TDA: Statistical Tools for Topological Data Analysis. Tools for the statistical analysis of persistent...
  • apTreeshape

  • Referenced in 8 articles [sw31620]
  • Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library...
  • COVAIN

  • Referenced in 1 article [sw10556]
  • combination of univariate and multivariate statistics, network topology and biochemical pathway mapping analysis ... multivariate statistical analysis, Granger time-series analysis, pathway mapping, correlation network topology analysis and visualization...
  • ergm.graphlets

  • Referenced in 4 articles [sw20899]
  • focus is on the addition of statistics based on graphlets. Graphlets are small, connected ... isomorphic induced subgraphs that describe the topological structure of a network. We introduce ... model terms that allows to incorporate statistics of any 2-, 3-, 4- and 5-node ... between nodal attributes (i.e., covariates) and local topologies around nodes...
  • TDAstats

  • Referenced in 1 article [sw31276]
  • comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent ... sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing ... persistent homology and statistical inference. The published form of TDAstats can be found in Wadhwa ... test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner...
  • topGO

  • Referenced in 3 articles [sw31859]
  • accounting for the topology of the GO graph. Different test statistics and different methods...
  • PhyML

  • Referenced in 11 articles [sw10915]
  • search the space of phylogenetic tree topologies, going from very fast and efficient methods ... evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate...
  • QNet

  • Referenced in 11 articles [sw19662]
  • together with a branch length for each topology. These branch lengths must be precomputed ... generating quartet weight data. GWeight utilizes statistical geometry [2] to generate quartet weights. LengthWeighter...
  • AFGen

  • Referenced in 17 articles [sw06325]
  • paths (PF), acyclic subgraphs (AF), and arbitrary topology subgraphs (GF). This vector-based representation ... retrieval show that these descriptors consistently and statistically outperform previously developed schemes based...
  • TreeFix

  • Referenced in 4 articles [sw29607]
  • TreeFix: statistically informed gene tree error correction using species trees. Accurate gene tree reconstruction ... information to confidently support one gene tree topology over many competing alternatives. Here, we present ... maximum-likelihood phylogenetic program), TreeFix finds a “statistically equivalent” gene tree that minimizes a species...
  • STARS

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

  • Referenced in 1 article [sw23836]
  • Gene Set Analysis Exploiting Pathway Topology. Implements topological gene set analysis using a two-step ... step clipper selects significant pathways according to statistical tests on the means and the concentration ... matrices of the graphs derived from pathway topologies. Then, it ”clips” the whole pathway identifying...
  • KDTREE

  • Referenced in 3 articles [sw18200]
  • multi-dimensional Euclidean space. Many data-based statistical algorithms require that one find near ... that vector space, usually with Euclidean topology. The k-d data structure and search algorithms...
  • 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...
  • topologyGSA

  • Referenced in 1 article [sw15178]
  • topologyGSA: Gene Set Analysis Exploiting Pathway Topology. Using Gaussian graphical models we propose a novel ... graph (a pathway) we introduce two statistical tests to compare the mean and the concentration...
  • PrimAlign

  • Referenced in 1 article [sw34148]
  • across species are sequentially similar and that topology of PPIs between orthologs is often conserved ... that PrimAlign outperforms several prevalent methods with statistically significant differences in multiple evaluation measures. PrimAlign ... synthetic networks and results suggest that popular topological measures do not reflect real precision...
  • GRETNA

  • Referenced in 1 article [sw26509]
  • huge complexity of network construction, analysis and statistics, toolboxes incorporating these functions are largely lacking ... graphical user interface (GUI); (ii) allowing topological analyses of global and local network properties with ... choice of thresholding procedure; (iv) allowing statistical comparisons of global, nodal and connectional network metrics...
  • NATbox

  • Referenced in 2 articles [sw32087]
  • open-source GUI implemented in the R statistical language for modelling and analysis ... acyclic graphs for visualization and investigate its topological properties using network analysis metrics, (iv) retrieve...
  • CytoNCA

  • Referenced in 2 articles [sw25624]
  • network, to integrate biological data with topological data to detect specific nodes. (iii) CytoNCA offers ... calculation results, and evaluate the accuracy by statistical measures. (v) Besides current eight centrality measures...