ToPASeq (version 1.6.0)

Package for Topology-based Pathway Analysis of RNASeq data

Description

Implementation of seven methods for topology-based pathway analysis of both RNASeq and microarray data: SPIA, DEGraph, TopologyGSA, TAPPA, PRS, PWEA and a visualization tool for a single pathway.

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Version

1.6.0

License

AGPL-3

Maintainer

Ivana Ihnatova

Last Published

February 15th, 2017

Functions in ToPASeq (1.6.0)

graphNEL2Pathway

Function to coerce a graphNEL to a Pathway

reduceGraph

Function to reduce the pathway graph

PWEA

Function to use PWEA method on microarray or RNA-Seq data

DEGraph

Function to use DEGraph method on microarray or RNA-Seq data

TAPPA

Function to use TAPPA method on microarray or RNA-Seq data

AdjacencyMatrix2Pathway

Function to coerce an adjacency matrix to a Pathway

preparePathways

Function to prepare pathways for topology-based pathway analysis

estimateCF

Function to estimate multi-subunit protein complexes and gene families in a pathway

ToPASeq-deprecated

Deprecated functions in package ‘ToPASeq’

makeDefautEdgeData

Creates auxiliary data needed for SPIA method

collectWeightsPRS

Function to calculate gene-level weights for topology-based pathway analysis

SPIA

Function to use SPIA method on microarray or RNA-Seq data

res

Function to extract parts of object

convertIdentifiersByVector

Function to convert identifiers in pathways by user specified vector

ToPASeq-package

Package for topology-based pathway analysis of microarray and RNASeq data

KEGG2Pathway

Function to parse KEGG KGML file into a Pathway

Pathway-method

Class "Pathway"

TopologyGSA

Function to use TopologyGSA method on microarray or RNA-Seq data

clipper

Function to use clipper method on microarray or RNA-Seq data

PRS

Function to use PRS method on microarray or RNA-Seq data