This is the development version of seq2pathway; for the stable release version, see seq2pathway.
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing dataBioconductor version: Development (3.22)
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 uchicago.edu>; Bin Wang <binw at uchicago.edu>
Maintainer: Arjun Kinstlick <akinstlick at uchicago.edu>
Citation (from within R, entercitation("seq2pathway")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("seq2pathway")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("seq2pathway")Follow Installation instructions to use this package in your R session.
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