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The accurate annotation of genes and Quantitative Trait Loci (QTLs) located within candidate markers and/or regions (haplotypes, windows, CNVs, etc) is a crucial step the most common genomic analyses performed in livestock, such as Genome-Wide Association Studies or transcriptomics. The Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package designed to provide an intuitive and straightforward environment to annotate positional candidate genes and QTLs from high-throughput genetic studies in livestock. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies, etc.), and QTL enrichment in different livestock species including cattle, pigs, sheep, and chicken, among others.
| Version: | 1.5 |
| Depends: | R (≥ 4.0.0) |
| Imports: | circlize, data.table, doParallel, dplyr, ggplot2, graphics, grDevices, foreach, lattice , parallel, RColorBrewer, rtracklayer, stats, stringr, unbalhaar, utils, DT, webshot, igraph, visNetwork, CompQuadForm, Matrix |
| Suggests: | Hmisc, knitr, rmarkdown, testthat |
| Published: | 2024-06-04 |
| DOI: | 10.32614/CRAN.package.GALLO |
| Author: | Pablo Fonseca [aut, cre], Aroa Suarez-Vega [aut], Gabriele Marras [aut], Angela Cánovas [aut] |
| Maintainer: | Pablo Fonseca <pfonseca at uoguelph.ca> |
| License: | GPL-3 |
| URL: | <https://github.com/pablobio/GALLO> |
| NeedsCompilation: | no |
| Citation: | GALLO citation info |
| Materials: | README NEWS |
| CRAN checks: | GALLO results |
| Reference manual: | GALLO.pdf |
| Vignettes: |
Genomic Annotation in Livestock for positional candidate LOci: GALLO |
| Package source: | GALLO_1.5.tar.gz |
| Windows binaries: | r-devel: GALLO_1.5.zip, r-release: GALLO_1.5.zip, r-oldrel: GALLO_1.5.zip |
| macOS binaries: | r-release (arm64): GALLO_1.5.tgz, r-oldrel (arm64): GALLO_1.5.tgz, r-release (x86_64): GALLO_1.5.tgz, r-oldrel (x86_64): GALLO_1.5.tgz |
| Old sources: | GALLO archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.