geneClusterPattern
Plot conserved gene pattern across multiple species
Bioconductor version: 3.24 · Package version: 0.99.2
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("geneClusterPattern")Details
| Maintainer | Jianhong Ou <jou@morgridge.org> |
| Author | Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>), Kenneth Poss [aut, fnd] |
| License | MIT + file LICENSE |
| URL | https://github.com/jianhong/geneClusterPattern |
| Bug Reports | https://github.com/jianhong/geneClusterPattern/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/geneClusterPattern/ |
Citation
From within R, enter citation("geneClusterPattern"):
Jianhong Ou, Kenneth Poss. geneClusterPattern: Plot conserved gene pattern across multiple species. doi:10.18129/B9.bioc.geneClusterPattern, R package version 0.99.2, https://bioconductor.org/packages/geneClusterPattern.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | geneClusterPattern_0.99.2.tar.gz |
| Windows binary (x86_64) | geneClusterPattern_0.99.2.zip |
| macOS binary (arm64) | geneClusterPattern_0.99.2.tgz |
| macOS binary (x86_64) | geneClusterPattern_0.99.2.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocGenerics, Biostrings, pwalign, GenomeInfoDb, GenomicRanges, grDevices, IRanges, RANN, biomaRt, grid, methods, Seqinfo, stats, trackViewer, utils
Suggests: org.Dr.eg.db, BiocStyle, knitr, rmarkdown, testthat, S4Vectors