Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 25979472.
- Also identified by DOI 10.1093/bioinformatics/btv289 and PMC identifier 4565027.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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. The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html. xyang2@uchicago.edu Supplementary data are available at Bioinformatics online.
Medical subject headings
- Computational Biology
- Genome, Human
- High-Throughput Nucleotide Sequencing
- Signal Transduction
- Software