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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ToPASeq")
In most cases, you don't need to download the package archive at all.
ToPASeq
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see ToPASeq.
Package for Topology-based Pathway Analysis of RNASeq data
Bioconductor version: 3.3
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 (from within R,
enter citation("ToPASeq")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ToPASeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ToPASeq")
| R Script | An R Package for topology-based pathway analysis of microaray and RNA-Seq data | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, NetworkEnrichment, Pathways, RNASeq, Software, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2 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 |
| LinkingTo | Rcpp |
| Suggests | RUnit, BiocGenerics, gageData, DEGraph, plotrix, org.Hs.eg.db |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ToPASeq_1.6.0.tar.gz |
| Windows Binary | ToPASeq_1.6.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | ToPASeq_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ToPASeq/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/ToPASeq/ |
| Package Downloads Report | Download Stats |
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