• HAP

  • Referenced in 33 articles [sw04870]
  • complexes in the context of topological data analysis...
  • Gudhi

  • Referenced in 11 articles [sw08777]
  • interest for computational topology is topological data analysis, where one is interested in learning topological ... complexes are implemented with a simplex tree data structure. The simplex tree is an efficient...
  • TDA

  • Referenced in 7 articles [sw15508]
  • package TDA: Statistical Tools for Topological Data Analysis. Tools for the statistical analysis of persistent...
  • Persistence Landscape

  • Referenced in 4 articles [sw21260]
  • persistence landscapes toolbox for topological statistics. Topological data analysis provides a multiscale description ... statistics and machine learning with topological data analysis. We present an experiment showing that...
  • jHoles

  • Referenced in 3 articles [sw15020]
  • persistent homology. Complex networks equipped with topological data analysis are one of the promising tools...
  • SimBa

  • Referenced in 3 articles [sw28063]
  • persistence via Simplicial Batch collapse. In topological data analysis, a point cloud data P extracted...
  • RIVET

  • Referenced in 2 articles [sw27770]
  • RIVET is a tool for topological data analysis, and more specifically, for the visualization...
  • TDAmapper

  • Referenced in 0 articles [sw15184]
  • Dimensional Data Using Discrete Morse Theory. Topological Data Analysis using Mapper (discrete Morse theory). Generate...
  • COVAIN

  • Referenced in 1 article [sw10556]
  • multivariate statistics, network topology and biochemical pathway mapping analysis is in all cases recommended. Therefore ... uploading data, data preprocessing, uni- and multivariate statistical analysis, Granger time-series analysis, pathway mapping ... correlation network topology analysis and visualization, and finally saving results in a user-friendly ... analysis of variance, principal components analysis, independent components analysis, clustering and correlation coefficient analysis...
  • ESOM-MAP

  • Referenced in 7 articles [sw12044]
  • distance functions, parameter cooling strategies, ESOM grid topologies, and neighborhood kernels. Visualization of high dimensional ... training process. Interactive, explorative data analysis and clustering by linking ESOM to the training data...
  • MScomplex

  • Referenced in 2 articles [sw21417]
  • Visual Analysis Using Morse-Smale Complexes. The Morse-Smale complex is a topological data structure ... applications that use this data structure for visualization and analysis of data from various scientific...
  • TADD

  • Referenced in 6 articles [sw02821]
  • TADD: A computational framework for data analysis using discrete Morse theory. This paper presents ... discrete Morse theory, which guarantees the topological consistency of the computed extremal structure. Using...
  • F-Tool

  • Referenced in 1 article [sw08742]
  • processing), numerical analysis, and result visualization (post-processing). An efficient, topology-based data representation scheme ... experience in using FTOOL in the Structural Analysis course in PUC-Rio, pointing...
  • MARMOSET

  • Referenced in 3 articles [sw14811]
  • particles. An OSET description of the data strongly constrains the underlying new physics, and sharply ... analysis of new-physics signals, especially when they arise from complicated production and decay topologies ... testing of theoretical hypotheses suggested by both data and model-building intuition, which together chart...
  • CytoNCA

  • Referenced in 1 article [sw25624]
  • Cytoscape plugin integrating calculation, evaluation and visualization analysis for multiple centrality measures. IMPLEMENTATION AND PERFORMANCE ... with topological data to detect specific nodes. (iii) CytoNCA offers multiple potent visualization analysis modules...
  • OCOTILLO

  • Referenced in 10 articles [sw09292]
  • presents algorithms, software development and computational complexity analysis for problems arising in the design ... OCOTILLO for combinatorial peptide design using real data libraries. The package provides exact solutions ... general inverse problems based on shortest-path topological indices. Our results are superior both...
  • Situs

  • Referenced in 4 articles [sw09515]
  • crystallography. A set of visualization and analysis procedures, termed the Situs package, has been developed ... protein subunits in low-resolution data. Topology-representing neural networks are employed to vector-quantize...
  • joda

  • Referenced in 2 articles [sw20391]
  • Joint Deregulation Analysis (JODA). joda is an R package implementing the JODA algorithm introduced ... algorithm takes as input perturbation data of the same regulators in two different cell populations ... context: known transcription factor targets and known topologies of signaling pathway (for both populations ... examples of differential genes. The differential expression analysis is performed using our approach implemented...
  • ANIMO

  • Referenced in 1 article [sw29381]
  • ANIMO (Analysis of Networks with Interactive MOdeling) is a tool for modeling biological signaling networks ... game, where the user ”plays” with the topology of a network to get a better ... network topologies by fitting them to experimental time series of protein activity data...
  • CONTOUR

  • Referenced in 1 article [sw23697]
  • topological analysis program. CONTOUR is a tool for studying the topology of large-scale structure ... discusses the application of CONTOUR to observational data sets and presents a complete listing...