Software & Tools
Open-source tools for the livestock research community
We develop open-source computational tools to support genomic and environmental research in livestock. All tools are freely available and designed to be accessible to researchers with varying levels of programming experience.
EnrichKit
EnrichKit is a comprehensive R-based tool designed for functional characterization of gene lists in livestock species. It maps genomic coordinates (from GWAS, RNA-seq, WGBS, etc.) to gene features and performs enrichment analysis using multiple biological databases including Gene Ontology (GO), KEGG pathways, InterPro domains, and medical subject headings.
Features
- Maps genomic coordinates to gene features using species-specific annotations
- Supports multiple livestock species (cattle, pig, chicken, sheep, horse)
- Performs over-representation analysis (ORA) and gene set enrichment analysis (GSEA)
- Integrates GO, KEGG, InterPro, and MeSH databases
- Handles data from SNP arrays, WGS, RNA-seq, WGBS, and ATAC-seq
- Generates publication-ready plots and summary tables
greenfeedr
greenfeedr is an R package that streamlines the processing and reporting of data collected from GreenFeed systems (C-Lock Inc.), which measure individual enteric methane (CH₄) and carbon dioxide (CO₂) emissions from ruminant animals. The package automates data cleaning, quality control, and summary statistics, reducing processing time and ensuring consistency across research groups.
Features
- Reads and parses raw GreenFeed output files
- Applies customizable quality control filters
- Calculates daily and period-level gas emission summaries
- Generates standardized reports and visualizations
- Supports multi-unit and multi-farm data
- Integrates with existing R-based analysis workflows