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:
GALLO_1.1.tar.gz
GALLO_1.1.zip(r-4.5)GALLO_1.1.zip(r-4.4)GALLO_1.1.zip(r-4.3)
GALLO_1.1.tgz(r-4.4-any)GALLO_1.1.tgz(r-4.3-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
Last updated 4 years agofrom:96f8b8f97f. Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Sep 09 2024 |
| R-4.5-win | WARNING | Sep 09 2024 |
| R-4.5-linux | WARNING | Sep 09 2024 |
| R-4.4-win | WARNING | Sep 09 2024 |
| R-4.4-mac | WARNING | Sep 09 2024 |
| R-4.3-win | WARNING | Sep 09 2024 |
| R-4.3-mac | WARNING | Sep 09 2024 |
Exports:find_genes_qtls_around_markersimport_gff_gtfoverlapping_among_groupsplot_overlappingplot_qtl_infoqtl_enrichQTLenrich_plotrelationship_plot
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbslibcachemcirclizeclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyrDTdynamicTreeCutevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2GlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigpromisesR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsrtracklayerS4ArraysS4VectorssassscalesshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyselecttinytexUCSC.utilsunbalhaarutf8vctrsviridisLitewithrxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Search genes and QTLs around candidate regions | find_genes_qtls_around_markers |
| Import .gtf and .gff files to be used during gene and QTL annotation, respectively | import_gff_gtf |
| Overlapping between grouping factors | overlapping_among_groups |
| Plot overlapping between data and grouping factors | plot_overlapping |
| Plot QTLs information from the find_genes_qtls_around_markers output | plot_qtl_info |
| Performs a QTL enrichment analysis based in a Bootstrap simulation for each QTL class | qtl_enrich |
| Plot enrichment results for QTL enrichment analysis | QTLenrich_plot |
| Plot relationship between data and grouping factors | relationship_plot |