Package: autoGO 0.9.1
Fabio Ticconi
autoGO: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations
Auto-GO is a framework that enables automated, high quality Gene Ontology enrichment analysis visualizations. It also features a handy wrapper for Differential Expression analysis around the 'DESeq2' package described in Love et al. (2014) <doi:10.1186/s13059-014-0550-8>. The whole framework is structured in different, independent functions, in order to let the user decide which steps of the analysis to perform and which plot to produce.
Authors:
autoGO_0.9.1.tar.gz
autoGO_0.9.1.zip(r-4.5)autoGO_0.9.1.zip(r-4.4)autoGO_0.9.1.zip(r-4.3)
autoGO_0.9.1.tgz(r-4.4-any)autoGO_0.9.1.tgz(r-4.3-any)
autoGO_0.9.1.tar.gz(r-4.5-noble)autoGO_0.9.1.tar.gz(r-4.4-noble)
autoGO_0.9.1.tgz(r-4.4-emscripten)autoGO_0.9.1.tgz(r-4.3-emscripten)
autoGO.pdf |autoGO.html✨
autoGO/json (API)
| # Install 'autoGO' in R: |
| install.packages('autoGO', repos = c('https://mpallocc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mpallocc/auto-go/issues
- comparisons - Example comparison data.
- counts - Example raw count data.
- groups - Example group data.
Last updated 9 months agofrom:8e56f1dfa6. Checks:OK: 6 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 04 2024 |
| R-4.5-win | OK | Nov 04 2024 |
| R-4.5-linux | WARNING | Nov 04 2024 |
| R-4.4-win | OK | Nov 04 2024 |
| R-4.4-mac | OK | Nov 04 2024 |
| R-4.3-win | OK | Nov 04 2024 |
| R-4.3-mac | OK | Nov 04 2024 |
Exports:autoGObarplotGOchoose_databasedeseq_analysisfiltering_DEheatmapGOlolliGOread_enrich_tablesread_gene_listsssgsea_wrappervolcanoplot
Dependencies:abindannotateAnnotationDbiapeaskpassassortheadbabelgenebeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64blobcachemcirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDESeq2dichromatdigestdoParalleldplyrenrichRfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegraphGSEABaseGSVAgtableHDF5ArrayhmshttrimguRIRangesirlbaisobanditeratorsjpegjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemsigdbrmunsellnlmeopensslopenxlsxpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrreshape2rhdf5rhdf5filtersRhdf5librjsonrlangRSQLitersvdS4ArraysS4VectorsScaledMatrixscalesshapeSingleCellExperimentslamsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystextshapetibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrWriteXLSXMLxtableXVectorzipzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| barplotGO | barplotGO |
| choose_database | choose_database |
| Example comparison data. | comparisons |
| Example raw count data. | counts |
| Differential Gene Expression Analysis | deseq_analysis |
| Filtering DESeq2 results | filtering_DE |
| Example group data. | groups |
| HeatmapGO | heatmapGO |
| lolliGO | lolliGO |
| Read enrichment results from tables | read_enrich_tables |
| Read all the genes lists | read_gene_lists |
| ssGSEA | ssgsea_wrapper |
| Volcano Plot | volcanoplot |
