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Seq2pathway：一个用于下一代测序数据通路分析的R/Bioconductor软件包。

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

作者信息

Wang Bin, Cunningham John M, Yang Xinan Holly

机构信息

Section of Hematology/Oncology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA.

出版信息

Bioinformatics. 2015 Sep 15;31(18):3043-5. doi: 10.1093/bioinformatics/btv289. Epub 2015 May 15.

DOI:10.1093/bioinformatics/btv289
PMID:25979472
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4565027/
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.

摘要

未标注

Seq2pathway是一个用于基因组位点通路（或功能基因集）分析的R/Python包装器，适用于基因组研究的进展。Seq2pathway将基因组位点的生物学意义与其靶转录本相关联，然后将基因水平上的量化值汇总为通路分数。它旨在从下一代测序（NGS）数据中分离出系统性干扰和常见的生物学基础。Seq2pathway为Bioconductor用户提供了更强的能力，以发现由编码基因和非编码元件的顺式调控共同引起的集体通路效应。

可用性和实现方式

该软件包可在http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html免费获取。

联系方式

xyang2@uchicago.edu

补充信息

补充数据可在《生物信息学》在线获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1389/4565027/1a853e942e3b/btv289f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1389/4565027/1a853e942e3b/btv289f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1389/4565027/1a853e942e3b/btv289f1p.jpg

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