Package: sitadela 1.15.0
Panagiotis Moulos
sitadela: An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported.
Authors:
sitadela_1.15.0.tar.gz
sitadela_1.15.0.zip(r-4.5)sitadela_1.15.0.zip(r-4.4)sitadela_1.15.0.zip(r-4.3)
sitadela_1.15.0.tgz(r-4.4-any)sitadela_1.15.0.tgz(r-4.3-any)
sitadela_1.15.0.tar.gz(r-4.5-noble)sitadela_1.15.0.tar.gz(r-4.4-noble)
sitadela_1.15.0.tgz(r-4.4-emscripten)sitadela_1.15.0.tgz(r-4.3-emscripten)
sitadela.pdf |sitadela.html✨
sitadela/json (API)
NEWS
| # Install 'sitadela' in R: |
| install.packages('sitadela', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pmoulos/sitadela/issues
On BioConductor:sitadela-1.15.0(bioc 3.21)sitadela-1.14.0(bioc 3.20)
softwareworkflowsteprnaseqtranscriptionsequencingtranscriptomicsbiomedicalinformaticsfunctionalgenomicssystemsbiologyalternativesplicingdataimportchipseq
Last updated 23 days agofrom:76eef2f472. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | WARNING | Nov 18 2024 |
| R-4.5-linux | WARNING | Nov 18 2024 |
| R-4.4-win | WARNING | Nov 18 2024 |
| R-4.4-mac | WARNING | Nov 18 2024 |
| R-4.3-win | WARNING | Nov 18 2024 |
| R-4.3-mac | WARNING | Nov 18 2024 |
Exports:addAnnotationaddCustomAnnotationgetAnnotationgetDbPathgetInstalledAnnotationsgetSeqInfogetUserAnnotationsimportCustomAnnotationloadAnnotationremoveAnnotationsetDbPathtestCustomBuildtestCustomGtftestEnsembltestEnsemblSimpletestKnownBuildtestUcsctestUcscAlltestUcscUtrtestUcscUtrAll
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build a local genomic regions annotation database | addAnnotation |
| Import custom annotation to existing or new sitadela annotation database from GTF file | addCustomAnnotation |
| Annotation downloader | getAnnotation |
| List installed sitadela annotations | getInstalledAnnotations |
| Retrieve sequence length and other information | getSeqInfo |
| Get and set sitadela default database path | getDbPath setDbPath |
| List installed custom user-defined sitadela annotations | getUserAnnotations |
| Import a metaseqR2 custom annotation element | importCustomAnnotation |
| Load a sitadela simple annotation element | loadAnnotation |
| Remove an annotation from a sitadela database | removeAnnotation |
| Query and database build testing functions | testCustomBuild testCustomGtf testEnsembl testEnsemblSimple testKnownBuild testUcsc testUcscAll testUcscUtr testUcscUtrAll |
