Package: seq2pathway
Type: Package
Title: a novel tool for functional gene-set (or termed as pathway)
        analysis of next-generation sequencing data
Version: 1.0.1
Date: 2015-09-18
Author: Xinan Yang <xyang2@uchicago.edu>; Bin Wang <binw@uchicago.edu>
Maintainer: Xinan Yang <xyang2@uchicago.edu> with contribution from Lorenzo Pesce <lpesce@uchicago.edu> and Ana Marija Sokovic <anamarija@uchicago.edu>
Depends: R (>= 2.10.0)
biocViews: Software
Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
Description: 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.  
License: GPL-2
Packaged: 2015-10-01 05:48:46 UTC; biocbuild
NeedsCompilation: no
Built: R 3.2.2; ; 2015-10-01 13:03:01 UTC; windows
