Package: OmaDB 2.29.0

Klara Kaleb

OmaDB: R wrapper for the OMA REST API

A package for the orthology prediction data download from OMA database.

Authors:Klara Kaleb

OmaDB_2.29.0.tar.gz
OmaDB_2.29.0.zip(r-4.7)OmaDB_2.29.0.zip(r-4.6)OmaDB_2.29.0.zip(r-4.5)
OmaDB_2.29.0.tgz(r-4.6-any)OmaDB_2.29.0.tgz(r-4.5-any)
OmaDB_2.29.0.tar.gz(r-4.7-any)OmaDB_2.29.0.tar.gz(r-4.6-any)
OmaDB_2.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OmaDB/json (API)

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

Bug tracker:https://github.com/dessimozlab/omadb/issues

Datasets:
  • group - An example OMA group object.
  • hog - An example HOG object.
  • orthologs - An example orthologs object.
  • pairs - An example genome alignment object.
  • protein - An example protein object.
  • sequence_annotation - An example dataframe containing GO annotations identified from a given sequence.
  • sequence_map - An example dataframe containing proteins identified from a given sequence.
  • taxonomy - An example newick format taxonomy object.
  • xref - An example xref object.

On BioConductor:OmaDB-2.29.0(bioc 3.24)OmaDB-2.28.0(bioc 3.23)

softwarecomparativegenomicsfunctionalgenomicsgeneticsannotationgofunctionalprediction

6.05 score 2 stars 5 scripts 2 mentions 22 exports 47 dependencies

Last updated from:e834177fa5. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR196
linux-devel-x86_64NOTE428
source / vignettesOK237
linux-release-x86_64NOTE479
macos-release-arm64NOTE295
macos-oldrel-arm64NOTE247
windows-develNOTE385
windows-releaseNOTE388
windows-oldrelNOTE347
wasm-releaseOK157

Exports:annotateSequenceformatTopGOgetAnnotationgetAttributegetDatagetGenomegetGenomeAlignmentgetGenomePairsgetHOGgetLocusgetObjectAttributesgetOMAGroupgetProteingetTaxonomygetTopGOgetTreegetVersiongetXrefmapSequenceresolveURLsearchProteinsetAPI

Dependencies:AnnotationDbiapeaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdigestfastmapgenericsGenomicRangesglueGO.dbgraphhttrIRangesjsonliteKEGGRESTlatticelifecyclematrixStatsmemoisemimenlmeopensslpkgconfigplyrpngR6RcpprlangRSQLiteS4VectorsSeqinfoSparseMsystopGOvctrsXVector

Sequence Analysis with OmaDB
Rendered fromsequence_mapping.Rmdusingknitr::rmarkdown

Last update: 2019-02-21
Started: 2017-10-12

Get started with OmaDB
Some useful functions | searchProtein | getGenomePairs | getProtein | getObjectAttributes | getAttribute | lazy loading
Rendered fromOmaDB.Rmdusingknitr::rmarkdown

Last update: 2019-02-21
Started: 2018-04-27

Exploring Hierarchical orthologous groups with OmaDB
The HOGs
Rendered fromexploring_hogs.Rmdusingknitr::rmarkdown

Last update: 2018-12-21
Started: 2017-10-12

Exploring Taxonomic trees with OmaDB
Rendered fromtree_visualisation.Rmdusingknitr::rmarkdown

Last update: 2018-12-21
Started: 2017-10-12

Readme and manuals

Help Manual

Help pageTopics
OmaDB: A package for the orthology prediction data download from OMA database.OmaDB-package OmaDB
Resolve URLs automatically when accessed$.omadb_obj
Map GO annotation to a sequence that is not available in the OMA BrowserannotateSequence
Format the GO annotations dataformatTopGO
Get the value for the Object AttributegetAttribute
Retrieve a genome from the OMA Browser databasegetGenome
Retrieves the pairwise relations among two genomesgetGenomePairs
Retrieve a HOG from the OMA BrowsergetHOG
Get loci for a given list of proteinsgetLocus
Get the Object AttributesgetObjectAttributes
Retrieve an OMA Group from the OMA BrowsergetOMAGroup
Retrieve a protein from the OMA BrowsergetProtein
Get the Taxonomic tree functiongetTaxonomy
Get the topGO Object functiongetTopGO
Get the Tree ObjectgetTree
Get the API and database version functiongetVersion
An example OMA group object.group
An example HOG object.hog
Map the Protein Sequence FunctionmapSequence
An example orthologs object.orthologs
An example genome alignment object.pairs
An example protein object.protein
Load data for a given url from the OMA Browser API.resolveURL
Get the CrossReferences in the OMA database for a patternsearchProtein
An example dataframe containing GO annotations identified from a given sequence.sequence_annotation
An example dataframe containing proteins identified from a given sequence.sequence_map
Set the url to the OMA Browser APIsetAPI
An example newick format taxonomy object.taxonomy
An example xref object.xref