ToPASeq
This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ToPASeq.
Topology-based pathway analysis of RNA-seq data
Bioconductor version: 3.10
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("ToPASeq")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ToPASeq")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ToPASeq")| Eight methods for topology-based pathway analysis of RNA-seq data | HTML | R Script |
| Topology-based pathway analysis of RNA-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, ImmunoOncology, NetworkEnrichment, Pathways, RNASeq, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | AGPL-3 |
| Depends | R (>= 3.5.0), graphite |
| Imports | Rcpp, graph, methods, Biobase, RBGL, SummarizedExperiment, gRbase, limma, corpcor |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR, plotrix, breastCancerVDX, EnrichmentBrowser |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ToPASeq_1.20.0.tar.gz |
| Windows Binary | ToPASeq_1.20.0.zip |
| Mac OS X 10.11 (El Capitan) | ToPASeq_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ToPASeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ToPASeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/ToPASeq/ |
| Package Short Url | https://bioconductor.org/packages/ToPASeq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |