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

 

   

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

Bioconductor version: Release (3.3)

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 R Script An R package for sequence
PDF   Reference Manual

Details

biocViews Software
Version 1.4.0
In Bioconductor since BioC 3.1 (R-3.2) (1.5 years)
License GPL-2
Depends R (>= 2.10.0)
Imports nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
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Package Archives

Follow Installation instructions to use this package in your R session.

Package Source seq2pathway_1.4.0.tar.gz
Windows Binary seq2pathway_1.4.0.zip
Mac OS X 10.9 (Mavericks) seq2pathway_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/seq2pathway/tree/release-3.3
Package Short Url http://bioconductor.org/packages/seq2pathway/
Package Downloads Report Download Stats

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