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

Bioinformatics (2015) 31(18) 3043-3045
DOI: 10.1093/bioinformatics/btv289
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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.

Figures

  • Fig. 1. The identification of biological process from 460 height-associated SNPs. (A) Results of both methods were comparable to the prediction of a comprehensive study on human height (Wood et al., 2014). (B) A demonstration of the case that both common and different genes are identified by two methods for the same GO term (GO:0006397). (C) Common and different SNPs are identified by two methods for the genes in Panel B. (D) Selective biological process terms identified by two or three methods, followed by the commonly identified (in black) and seq2pathway specifically identified (in blue, underlined) genes and SNPs shown in panels B–C.

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CITATION STYLE

APA

Wang, B., Cunningham, J. M., & Yang, X. (2015). Seq2pathway: An R/Bioconductor package for pathway analysis of next-generation sequencing data. Bioinformatics, 31(18), 3043–3045. https://doi.org/10.1093/bioinformatics/btv289

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