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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ToPASeq")
In most cases, you don't need to download the package archive at all.
ToPASeq
Package for Topology-based Pathway Analysis of RNASeq data
Bioconductor version: 3.0
Implementation of seven methods for topology-based pathway analysis of both RNASeq and microarray data: SPIA, DEGraph, TopologyGSA, TAPPA, TBS, 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:
source("http://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 | 1.0.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | AGPL-3 |
| Depends | graphite, gRbase, graph, locfit |
| Imports | R.utils, edgeR, DESeq2, GenomicRanges, igraph, DESeq, fields, limma, TeachingDemos, SPIA, clipper, topologyGSA |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, gageData, Rgraphviz, DEGraph |
| 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_1.0.1.tar.gz |
| Windows Binary | ToPASeq_1.0.1.zip |
| Mac OS X 10.6 (Snow Leopard) | ToPASeq_1.0.1.tgz |
| Mac OS X 10.9 (Mavericks) | ToPASeq_1.0.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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