ToPASeq

DOI: 10.18129/B9.bioc.ToPASeq    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Topology-based pathway analysis of RNA-seq data

Bioconductor version: Release (3.13)

Implementation of methods for topology-based pathway analysis of RNA-seq data. This includes Topological Analysis of Pathway Phenotype Association (TAPPA; Gao and Wang, 2007), PathWay Enrichment Analysis (PWEA; Hung et al., 2010), and the Pathway Regulation Score (PRS; Ibrahim et al., 2012).

Author: Ivana Ihnatova, Eva Budinska, Ludwig Geistlinger

Maintainer: Ivana Ihnatova <ihnatova at iba.muni.cz>

Citation (from within R, enter citation("ToPASeq")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ToPASeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, ImmunoOncology, NetworkEnrichment, Pathways, RNASeq, Software, Visualization
Version 1.26.0
In Bioconductor since BioC 3.0 (R-3.1) (7 years)
License AGPL-3
Depends R (>= 3.5.0), graphite
Imports Rcpp, graph, methods, Biobase, RBGL, SummarizedExperiment, gRbase, limma, corpcor
LinkingTo Rcpp
Suggests BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR, plotrix, breastCancerVDX, EnrichmentBrowser
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/ToPASeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ToPASeq
Package Short Url https://bioconductor.org/packages/ToPASeq/
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