seq2pathway
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see seq2pathway.
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
Bioconductor version: 3.12
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 Jennifer Sun <ysunn98 at gmail.com>
citation("seq2pathway")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| An R package for sequence | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL-2 |
| Depends | R (>= 3.5.0) |
| Imports | nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data |
| System Requirements | Python3 with packages future, builtins, past.utils, bisect, datetime, shutil, and functools |
| URL |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | seq2pathway_1.22.0.tar.gz |
| Windows Binary | seq2pathway_1.22.0.zip |
| macOS 10.13 (High Sierra) | seq2pathway_1.22.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |