
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 timeseries analysis, pathway mapping ... correlation network topology analysis and visualization, and finally saving results in a userfriendly ... analysis of variance, principal components analysis, independent components analysis, clustering and correlation coefficient analysis...

ESOMMAP
 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 MorseSmale Complexes. The MorseSmale 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...

FTool
 Referenced in 1 article
[sw08742]
 processing), numerical analysis, and result visualization (postprocessing). An efficient, topologybased data representation scheme ... experience in using FTOOL in the Structural Analysis course in PUCRio, pointing...

MARMOSET
 Referenced in 3 articles
[sw14811]
 particles. An OSET description of the data strongly constrains the underlying new physics, and sharply ... analysis of newphysics signals, especially when they arise from complicated production and decay topologies ... testing of theoretical hypotheses suggested by both data and modelbuilding 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 shortestpath 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 lowresolution data. Topologyrepresenting neural networks are employed to vectorquantize...

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 largescale structure ... discusses the application of CONTOUR to observational data sets and presents a complete listing...