To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("seq2pathway")

In most cases, you don't need to download the package archive at all.

seq2pathway

   

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see seq2pathway.

a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data

Bioconductor version: 3.2

Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.

Author: Xinan Yang <xyang2 at uchicago.edu>; Bin Wang <binw at uchicago.edu>

Maintainer: Xinan Yang <xyang2 at uchicago.edu> with contribution from Lorenzo Pesce <lpesce at uchicago.edu> and Ana Marija Sokovic <anamarija at uchicago.edu>

Citation (from within R, enter citation("seq2pathway")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("seq2pathway")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("seq2pathway")

 

PDF An R package for sequence
PDF   Reference Manual
Text   NEWS

Details

biocViews Software
Version 1.2.0
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License GPL-2
Depends R (>= 2.10.0)
Imports nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
LinkingTo
Suggests
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 seq2pathway_1.2.0.tar.gz
Windows Binary seq2pathway_1.2.0.zip
Mac OS X 10.6 (Snow Leopard) seq2pathway_1.2.0.tgz
Mac OS X 10.9 (Mavericks) seq2pathway_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/seq2pathway/tree/release-3.2
Package Short Url http://bioconductor.org/packages/seq2pathway/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center