Package: seq2pathway
Type: Package
Title: a novel tool for functional gene-set (or termed as pathway)
        analysis of next-generation sequencing data
Version: 1.45.0
Date: 2021-11-21
Author: Xinan Yang <xyang2@uchicago.edu>; Bin Wang <binw@uchicago.edu>
Maintainer: Arjun Kinstlick <akinstlick@uchicago.edu>
Depends: R (>= 3.6.2)
biocViews: Software
Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
Description: 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.
License: GPL-2
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:40:28 UTC
RemoteUrl: https://github.com/bioc/seq2pathway
RemoteRef: HEAD
RemoteSha: ff835e8a3c4bc21fe50dd9dccd0c7a73f35eac35
NeedsCompilation: no
Packaged: 2026-07-04 05:25:43 UTC; root