This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ToPASeq.
Bioconductor version: 3.8
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: Ludwig Geistlinger <ludwig.geistlinger at sph.cuny.edu>
Citation (from within R,
enter citation("ToPASeq")
):
To install this package, start R (version "3.5") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ToPASeq")
HTML | R Script | Topology-based pathway analysis of RNA-seq data |
Reference Manual | ||
Text | NEWS |
biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, ImmunoOncology, NetworkEnrichment, Pathways, RNASeq, Software, Visualization |
Version | 1.16.1 |
In Bioconductor since | BioC 3.0 (R-3.1) (4.5 years) |
License | AGPL-3 |
Depends | R (>= 3.5.0), graphite |
Imports | Rcpp, graph, methods |
LinkingTo | Rcpp |
Suggests | BiocStyle, EnrichmentBrowser, airway, knitr, rmarkdown |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | ToPASeq_1.16.1.tar.gz |
Windows Binary | ToPASeq_1.16.1.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | ToPASeq_1.16.1.tgz |
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 | http://bioconductor.org/packages/ToPASeq/ |
Package Downloads Report | Download Stats |
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