seq2pathway

DOI: 10.18129/B9.bioc.seq2pathway    

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

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("seq2pathway")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("seq2pathway")

 

PDF	R Script	An R package for sequence
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software
Version	1.24.0
In Bioconductor since	BioC 3.1 (R-3.2) (6.5 years)
License	GPL-2
Depends	R (>= 3.6.2)
Imports	nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	seq2pathway_1.24.0.tar.gz
Windows Binary	seq2pathway_1.24.0.zip
macOS 10.13 (High Sierra)	seq2pathway_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seq2pathway
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seq2pathway
Package Short Url	https://bioconductor.org/packages/seq2pathway/
Package Downloads Report	Download Stats