ToPASeq
This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ToPASeq.
Package for Topology-based Pathway Analysis of RNASeq data
Bioconductor version: 3.6
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.
Author: Ivana Ihnatova, Eva Budinska
Maintainer: Ivana Ihnatova <ihnatova at iba.muni.cz>
citation("ToPASeq")):
Installation
To install this package, start R (version "3.4") 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")| An R Package for topology-based pathway analysis of microaray and RNA-Seq data | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, NetworkEnrichment, Pathways, RNASeq, Software, Visualization |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | AGPL-3 |
| Depends | graphite(>= 1.16), gRbase, graph, locfit, Rgraphviz |
| Imports | R.utils, methods, Biobase, parallel, edgeR, DESeq2, SummarizedExperiment, RBGL, DESeq, fields, limma, TeachingDemos, KEGGgraph, qpgraph, clipper, AnnotationDbi, doParallel |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, gageData, DEGraph, plotrix, org.Hs.eg.db |
| 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_1.11.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| 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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |