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 (3.24)
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("seq2pathway")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Software |
| Version | 1.45.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.6.2) |
| Imports | nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data |
| System Requirements | |
| 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_1.45.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | seq2pathway_1.45.0.tgz |
| macOS Binary (sonoma-arm64) | seq2pathway_1.45.0.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 |