title: Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.
abstract: 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.
  
  
  METHODS
  The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html.
  
  
  BACKGROUND
  xyang2@uchicago.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Section of Hematology/Oncology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.affiliation: Section of Hematology/Oncology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Cunningham
authors.affiliation: Section of Hematology/Oncology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA.
authors.forename: Xinan Holly
authors.initials: XH
authors.lastname: Yang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D015398:Signal Transduction; D012984:Software; D014584:User-Computer Interface