To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("seq2pathway")
In most cases, you don't need to download the package archive at all.
Bioconductor version: Release (3.5)
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: Xinan Yang <xyang2 at uchicago.edu> with contribution from Lorenzo Pesce <lpesce at uchicago.edu> and Ana Marija Sokovic <anamarija at uchicago.edu>
Citation (from within R,
enter citation("seq2pathway")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("seq2pathway")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("seq2pathway")
R Script | An R package for sequence | |
Reference Manual | ||
Text | NEWS |
biocViews | Software |
Version | 1.8.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (2.5 years) |
License | GPL-2 |
Depends | R (>= 2.10.0) |
Imports | nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data |
LinkingTo | |
Suggests | |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | seq2pathway_1.8.0.tar.gz |
Windows Binary | seq2pathway_1.8.0.zip |
Mac OS X 10.11 (El Capitan) | seq2pathway_1.8.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/seq2pathway |
Package Short Url | http://bioconductor.org/packages/seq2pathway/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: