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seq2pathway

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 data


Bioconductor version: Development (3.20)

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, enter citation("seq2pathway")):

Installation

To install this package, start R (version "4.4") 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.

Documentation

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

browseVignettes("seq2pathway")
An R package for sequence PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Software
Version 1.37.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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_1.37.0.tar.gz
Windows Binary seq2pathway_1.37.0.zip
macOS Binary (x86_64) seq2pathway_1.37.0.tgz
macOS Binary (arm64) seq2pathway_1.37.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/seq2pathway
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/seq2pathway
Bioc Package Browser https://code.bioconductor.org/browse/seq2pathway/
Package Short Url https://bioconductor.org/packages/seq2pathway/
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