DOI: 10.18129/B9.bioc.seq2pathway    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see seq2pathway.

a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data

Bioconductor version: 3.12

Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.

Author: Xinan Yang <xyang2 at>; Bin Wang <binw at>

Maintainer: Xinan Yang <xyang2 at> with contribution from Jennifer Sun <ysunn98 at>

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biocViews Software
Version 1.22.0
In Bioconductor since BioC 3.1 (R-3.2) (6 years)
License GPL-2
Depends R (>= 3.5.0)
Imports nnet, WGCNA, GSA, biomaRt, GenomicRanges,
SystemRequirements Python3 with packages future, builtins, past.utils, bisect, datetime, shutil, and functools
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