geneClusterPattern
This is the development version of geneClusterPattern; to use it, please install the devel version of Bioconductor.
Plot conserved gene pattern across multiple species
Bioconductor version: Development (3.24)
An R package for constructing and comparing ortholog gene patterns around a focal gene across species. It enables the exploration of conserved gene neighborhoods (synteny) by organizing orthologous genes within a defined genomic window and aligning their relative positions across multiple genomes. It can retrieve homologous gene directly from Ensembl or it can incorporate user-provided ortholog group assignments.
Author: Jianhong Ou [aut, cre]
, Kenneth Poss [aut, fnd]
Maintainer: Jianhong Ou <jou at morgridge.org>
citation("geneClusterPattern")):
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("geneClusterPattern")
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("geneClusterPattern")| geneClusterPattern Vignette: overview | HTML | R Script |
| Reference Manual |
Details
| biocViews | Software, Visualization |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | BiocGenerics, Biostrings, pwalign, GenomeInfoDb, GenomicRanges, grDevices, IRanges, RANN, biomaRt, grid, methods, Seqinfo, stats, trackViewer, utils |
| System Requirements | |
| URL | https://github.com/jianhong/geneClusterPattern |
| Bug Reports | https://github.com/jianhong/geneClusterPattern/issues |
See More
| Suggests | org.Dr.eg.db, BiocStyle, knitr, rmarkdown, testthat, S4Vectors |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | geneClusterPattern_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | geneClusterPattern_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/geneClusterPattern |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/geneClusterPattern |
| Bioc Package Browser | https://code.bioconductor.org/browse/geneClusterPattern/ |
| Package Short Url | https://bioconductor.org/packages/geneClusterPattern/ |
| Package Downloads Report | Download Stats |