Introduction | Installation | Loading data | Differential Gene Expression | Parameters: | Filtering DESeq2 results | Volcano Plot | Choose of database | Reading gene lists | Enrichment analysis | Reading enrichment tables | Visualization: | Barplot | Lollipop | HeatmapGO | Single-sample Gene Set Enrichment Analysis
Package: autoGO 1.0.3
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_1.0.3.tar.gz
autoGO_1.0.3.zip(r-4.7-any)autoGO_1.0.3.zip(r-4.6-any)autoGO_1.0.3.zip(r-4.5-any)
autoGO_1.0.3.tgz(r-4.6-any)autoGO_1.0.3.tgz(r-4.5-any)
autoGO_1.0.3.tar.gz(r-4.7-any)autoGO_1.0.3.tar.gz(r-4.6-any)
autoGO_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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
Datasets:
- comparisons - Example comparison data.
- counts - Example raw count data.
- groups - Example group data.
Last updated from:410b61efb6. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 411 | ||
| source / vignettes | OK | 260 | ||
| linux-release | OK | 398 | ||
| macos-release | OK | 416 | ||
| macos-oldrel | OK | 329 | ||
| windows-devel | OK | 344 | ||
| windows-release | OK | 313 | ||
| windows-oldrel | OK | 308 | ||
| wasm-release | OK | 201 |
Exports:autoGObarplotGOchoose_databasedeseq_analysisfiltering_DEheatmapGOlolliGOread_enrich_tablesread_gene_listsssgsea_wrappervolcanoplot
Dependencies:abindannotateAnnotationDbiapeaskpassassertthatassortheadbabelgenebeachmatBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocParallelBiocSingularBiostringsbitbit64blobcachemcirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDESeq2dichromatdigestdir.expirydoParalleldplyrenrichRfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegraphGSEABaseGSVAgtableh5mreadHDF5Arrayhmshttrhttr2IRangesirlbaisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisememusemimemsigdbrnlmeopensslopenxlsxpillarpkgconfigplyrpngprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrreshape2rhdf5rhdf5filtersRhdf5librjsonrlangRSQLitersvdS4ArraysS4VectorsS7ScaledMatrixscalesSeqinfoshapeSingleCellExperimentslamsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystextshapetibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrWriteXLSXMLxtableXVectorzip
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 |