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Showing results 1 to 10 of 11.


Function ISOTopologyLevel [geometa v0.6-3]
keywords
topology
title
ISOTopologyLevel
description
ISOTopologyLevel
Function analyze.rwty [rwty v1.0.2]
keywords
topology,
title
analyze.rwty, the main interface for rwty analyses and plots.
description
This is the main user interface to rwty. It allows users to conduct simple visualizations of MCMC chain performance with very few arguments.
Function assortativity [EGAD v1.0.3]
keywords
topology
title
Calculating network assortativity
description
The function calculates the assortativity of a network, that measures the preference of interactions between similar nodes. As in most literature, 'similarity' is here defined in terms of node degrees.
Function runClipper [graphite v1.18.0]
keywords
topology
title
Run a topological analysis on an expression dataset using clipper.
description
clipper is a package for topological gene set analysis. It implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to reconstruct the most relevant signal path. In the first 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 the signal paths having the greatest association with a specific phenotype.
Function runDEGraphMulti [graphite v1.18.0]
keywords
topology
title
Run a topological analysis on an expression dataset using DEGraph package.
description
This function is deprecated and will be removed in a future release. You can use runDEGraph instead.
Function runSPIA [graphite v1.18.0]
keywords
topology
title
Run SPIA analysis
description
Run a topological analysis on an expression dataset using SPIA.
Function runDEGraph [graphite v1.18.0]
keywords
topology
title
Run a topological analysis on an expression dataset using DEGraph package.
description
DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions.
Function runClipperMulti [graphite v1.18.0]
keywords
topology
title
Run a topological analysis on an expression dataset using clipper.
description
This function is deprecated and will be removed in a future release. You can use runClipper instead.
Function runTopologyGSAMulti [graphite v1.18.0]
keywords
topology
title
Run a topological analysis on an expression dataset using topologyGSA.
description
This function is deprecated and will be removed in a future release. You can use runTopologyGSA instead.
Function runTopologyGSA [graphite v1.18.0]
keywords
topology
title
Run a topological analysis on an expression dataset using topologyGSA.
description
Use graphical models to test the pathway components highlighting those involved in its deregulation.