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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.

SUBMITTER: Wang B

PROVIDER: S-EPMC4565027 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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

Wang Bin B Cunningham John M JM Yang Xinan Holly XH

Bioinformatics (Oxford, England) 20150515 18

<h4>Unlabelled</h4>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 us ...[more]

PMID: 25979472

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