Package: Ularcirc 1.25.0
David Humphreys
Ularcirc: Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.
Authors:
Ularcirc_1.25.0.tar.gz
Ularcirc_1.25.0.zip(r-4.5)Ularcirc_1.25.0.zip(r-4.4)Ularcirc_1.25.0.zip(r-4.3)
Ularcirc_1.25.0.tgz(r-4.4-any)Ularcirc_1.25.0.tgz(r-4.3-any)
Ularcirc_1.25.0.tar.gz(r-4.5-noble)Ularcirc_1.25.0.tar.gz(r-4.4-noble)
Ularcirc_1.25.0.tgz(r-4.4-emscripten)Ularcirc_1.25.0.tgz(r-4.3-emscripten)
Ularcirc.pdf |Ularcirc.html✨
Ularcirc/json (API)
NEWS
| # Install 'Ularcirc' in R: |
| install.packages('Ularcirc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Ularcirc-1.25.0(bioc 3.21)Ularcirc-1.24.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
datarepresentationvisualizationgeneticssequencingannotationcoveragealternativesplicingdifferentialsplicing
Last updated 2 months agofrom:a6da8769c9. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | WARNING | Dec 19 2024 |
| R-4.5-linux | WARNING | Dec 19 2024 |
| R-4.4-win | WARNING | Dec 19 2024 |
| R-4.4-mac | WARNING | Dec 19 2024 |
| R-4.3-win | WARNING | Dec 19 2024 |
| R-4.3-mac | WARNING | Dec 19 2024 |
Exports:BSJ_detailsbsj_fastq_generatebsj_to_circRNA_sequencechimericStatsCompatible_Annotation_DBsFilterChimericJuncsloadSTAR_chimericplot_AllJunctionsRAD_scoreSelectUniqueJunctionsUlarcirc
Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebslibcachemclicodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrDTevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggplotifyggrepelgluegridGraphicsgsubfngtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemirbase.dbmomentsmunsellnlmeopensslOrganism.dplyrpillarpkgconfigplogrplotgardenerplyrangespngpromisesprotopurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesshinyshinydashboardshinyFilesshinyjssnowsourcetoolsSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlyulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BSJ_details This function returns details of a BSJ string and returns a list of coordinates. Can accept two different formats, Ularcirc or generic. | BSJ_details |
| bsj_fastq_generate | bsj_fastq_generate |
| bsj_to_circRNA_sequence | bsj_to_circRNA_sequence |
| chimericFilters | chimericFilters |
| chimericStats | chimericStats |
| Compatible_Annotation_DBs | Compatible_Annotation_DBs |
| Wrapper function for Ularcirc shiny app which expects a list of objects to be returned | FilterChimeric_Ularcirc |
| FilterChimericJuncs | FilterChimericJuncs |
| Grab_BS_Junc_Sequence | Junction_Sequence_from_Genome |
| loadSTAR_chimeric | loadSTAR_chimeric |
| plot_AllJunctions | plot_AllJunctions |
| RAD_score | RAD_score |
| SelectUniqueJunctions | SelectUniqueJunctions |
| sequence_from_exon_coords | sequence_from_exon_coords |
| Ularcirc | Ularcirc |
