DOI: 10.18129/B9.bioc.seq2pathway    

This is the development version of seq2pathway; for the stable release version, see seq2pathway.

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

Bioconductor version: Development (3.8)

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>; Bin Wang <binw at>

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

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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



PDF R Script An R package for sequence
PDF   Reference Manual
Text   NEWS


biocViews Software
Version 1.13.0
In Bioconductor since BioC 3.1 (R-3.2) (3 years)
License GPL-2
Depends R (>= 2.10.0)
Imports nnet, WGCNA, GSA, biomaRt, GenomicRanges,
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package seq2pathway_1.13.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) seq2pathway_1.13.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

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