GALLO: An R package for Genomic Annotation and integration of multiple data source in livestock for positional candidate LOci

Dataset type: Genomic, Software, Workflow, Bioinformatics, Data-Mining
Data released on November 23, 2020

Fonseca PAS; Suárez-Vega A; Marras G; Cánovas A (2020): GALLO: An R package for Genomic Annotation and integration of multiple data source in livestock for positional candidate LOci GigaScience Database. http://dx.doi.org/10.5524/100834

DOI10.5524/100834

The development of high-throughput sequencing and genotyping methodologies allowed the identification of thousands of genomic regions associated with several complex traits. The integration of multiple sources of biological information is a crucial step required to better understand patterns regulating the development of these traits. Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package developed for the accurate annotation of genes and quantitative trait loci (QTLs) located in regions identified in common genomic analyses performed in livestock, such as Genome-Wide Association Studies and transcriptomics using RNA-Sequencing. 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 chickens, etc. Consequently, GALLO is a useful package for the annotation, identification of hidden patterns across datasets, datamining previously reported associations, as well as the efficient scrutinization of the genetic architecture of complex traits in livestock.

Additional details

Read the peer-reviewed publication(s):


Additional information:

https://cran.r-project.org/web/packages/GALLO/vignettes/GALLO.html

https://rpubs.com/pablo_bio/GALLO_vignette

Github links:

https://github.com/pablobio/GALLO





File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivezip1.29 MB2020-11-18
readme.txtTEXT2.66 KB2020-11-23
Tabular DataTEXT5.08 KB2020-11-18
Tabular DataTEXT65.79 KB2020-11-18
Tabular DataTEXT1.13 MB2020-11-18
Tabular DataTEXT34.24 KB2020-11-18
Displaying 1-6 of 6 File(s).
Funding body Awardee Award ID Comments
Beef Cattle Research Council (BCRC) A Cánovas Sustainable Beef and Forage Science Cluster
Beef Cattle Research Council (BCRC) A Cánovas Beef Cattle Check-Off
Agriculture and Agri-Food Canada A Cánovas FDE.13.17 Canadian Agricultural Partnership
Date Action
November 23, 2020 Dataset publish
November 23, 2020 File GALLO-master.zip updated
November 23, 2020 File Supplementary_Table1.txt updated
November 23, 2020 File Supplementary_Table2.txt updated
November 23, 2020 File Supplementary_Table3.txt updated
November 23, 2020 File Supplementary_Table4.txt updated
November 24, 2020 Dataset publish
December 14, 2020 Manuscript Link added : 10.1093/gigascience/giaa149