Package: GALLO 1.1

Pablo Fonseca

GALLO: Genomic Annotation in Livestock for Positional Candidate LOci

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.

Authors:Pablo Fonseca [aut, cre], Aroa Suarez-Vega [aut], Gabriele Marras [aut], Angela Cánovas [aut]

GALLO_1.1.tar.gz
GALLO_1.1.zip(r-4.5)GALLO_1.1.zip(r-4.4)
GALLO_1.1.tgz(r-4.5-any)GALLO_1.1.tgz(r-4.4-any)
GALLO_1.1.tar.gz(r-4.5-noble)GALLO_1.1.tar.gz(r-4.4-noble)
GALLO_1.1.tgz(r-4.4-emscripten)GALLO_1.1.tgz(r-4.3-emscripten)
GALLO.pdf |GALLO.html
GALLO/json (API)
NEWS

# Install 'GALLO' in R:
install.packages('GALLO', repos = c('https://pablobio.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pablobio/gallo/issues

On CRAN:

Conda:

software

4.33 score 10 stars 3 scripts 1.1k downloads 4 mentions 8 exports 114 dependencies

Last updated 4 years agofrom:96f8b8f97f. Checks:1 ERROR, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesFAILMar 08 2025
R-4.5-winWARNINGMar 08 2025
R-4.5-macWARNINGMar 08 2025
R-4.5-linuxWARNINGMar 08 2025
R-4.4-winWARNINGMar 08 2025
R-4.4-macWARNINGMar 08 2025
R-4.4-linuxWARNINGMar 08 2025

Exports:find_genes_qtls_around_markersimport_gff_gtfoverlapping_among_groupsplot_overlappingplot_qtl_infoqtl_enrichQTLenrich_plotrelationship_plot

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbslibcachemcirclizeclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyrDTdynamicTreeCutevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2GlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigpromisesR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsrtracklayerS4ArraysS4VectorssassscalesshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyselecttinytexUCSC.utilsunbalhaarutf8vctrsviridisLitewithrxfunXMLXVectoryaml