geneClusterPattern

geneClusterPattern is 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.

Overview

Understanding how gene order is conserved across species provides insight into genome evolution and functional relationships between genes. geneClusterPattern facilitates this by building ortholog gene patterns centered on a gene of interest and comparing their surrounding genomic context across species.

The package supports two main sources of orthology information:

  • Homolog retrieval from Ensembl (via Compara)
  • Ortholog group assignments from OrthoFinder

These inputs are used to reconstruct ordered gene neighborhoods and generate comparable ortholog patterns across species.

Features

  • Retrieve homologs directly from Ensembl
  • Support orthogroup input from OrthoFinder
  • Construct gene patterns around a focal gene
  • Configurable upstream and downstream window size
  • Multi-species comparison
  • Tidy, analysis-friendly output
  • Visualization-ready structure for plotting gene patterns

Installation 

if (!require("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install('geneClusterPattern')
# or install from github for the development version
BiocManager::install('jianhong/geneClusterPattern')

Use Cases

  • Conserved synteny analysis
  • Comparative genomics
  • Evolution of gene clusters
  • Functional context of genes
  • Cross-species genome organization studies

Documentation

To view documentation of geneClusterPattern, start R and enter:

{r} browseVignettes('geneClusterPattern')

The documentation are also available online.

Contributions and Support

If you would like to contribute to this package, the standard workflow is as follows:

  1. Check that there isn’t already an issue about your idea in the jianhong/geneClusterPattern/issues to avoid duplicating work. If there isn’t one already, please create one so that others know you’re working on this
  2. Fork the jianhong/geneClusterPattern to your GitHub account
  3. Make the necessary changes / additions within your forked repository following Bioconductor contribution
  4. Use devtools::build and devtools::check to check the package work properly.
  5. Submit a Pull Request against the devel or current RELEASE_VERSION branch and wait for the code to be reviewed and merged.

If you’re not used to this workflow with git, you can start with some docs from GitHub or even their excellent git resources.

For further information or help, don’t hesitate to create a new issues at jianhong/geneClusterPattern/issues.

Reporting bug/issues

Many thanks for taking an interest in improving this package. Please report bug/issues at jianhong/geneClusterPattern/issues.