Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data

Abstract

UNLABELLED: Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores. It is designed to isolate systematic disturbances and common biological underpinnings from next-generation sequencing (NGS) data. Seq2pathway offers Bioconductor users enhanced capability in discovering collective pathway effects caused by both coding genes and cis-regulation of non-coding elements. AVAILABILITY AND IMPLEMENTATION: The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html. CONTACT: xyang2@uchicago.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.