Package: EpiTxDb 1.19.0
Felix G.M. Ernst
EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface
EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with.
Authors:
EpiTxDb_1.19.0.tar.gz
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EpiTxDb_1.19.0.tgz(r-4.4-any)EpiTxDb_1.19.0.tgz(r-4.3-any)
EpiTxDb_1.19.0.tar.gz(r-4.5-noble)EpiTxDb_1.19.0.tar.gz(r-4.4-noble)
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EpiTxDb.pdf |EpiTxDb.html✨
EpiTxDb/json (API)
NEWS
| # Install 'EpiTxDb' in R: |
| install.packages('EpiTxDb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/felixernst/epitxdb/issues
- rmbase_data - EpiTxDb internal data
On BioConductor:EpiTxDb-1.19.0(bioc 3.21)EpiTxDb-1.18.0(bioc 3.20)
Last updated 2 months agofrom:49a7f33f47. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 26 2024 |
| R-4.5-win | WARNING | Nov 26 2024 |
| R-4.5-linux | WARNING | Dec 26 2024 |
| R-4.4-win | WARNING | Nov 26 2024 |
| R-4.4-mac | WARNING | Dec 26 2024 |
| R-4.3-win | WARNING | Nov 26 2024 |
| R-4.3-mac | WARNING | Dec 26 2024 |
Exports:as.listcolumnsdownloadRMBaseFilesEPITXDB_RMBASE_URLgetRMBaseDataAsGRangesgettRNAdbDataAsGRangeskeyskeytypeslistAvailableGenomesFromRMBaselistAvailableModFromRMBaselistAvailableOrganismsFromRMBaselistAvailableOrganismsFromtRNAdbmakeEpiTxDbmakeEpiTxDbFromGRangesmakeEpiTxDbFromRMBasemakeEpiTxDbFromRMBaseFilesmakeEpiTxDbFromtRNAdbmodificationsmodificationsBymodifiedSeqsByTranscriptorganismpositionSequencerescaleselectseqinfoseqlevelsshiftGenomicToTranscriptshiftTranscriptToGenomic
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeModstringsmunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRCurlrestfulrrexRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrStructstringsSummarizedExperimentsystibbletidyrtidyselecttRNAtRNAdbImporttxdbmakerUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryamlzlibbioc
EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface
Rendered fromEpiTxDb.Rmdusingknitr::rmarkdownon Dec 26 2024.Last update: 2021-03-25
Started: 2020-02-06
EpiTxDb: creating an EpiTxDb object
Rendered fromEpiTxDb-creation.Rmdusingknitr::rmarkdownon Dec 26 2024.Last update: 2024-03-24
Started: 2020-02-26
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| EpiTxDb objects | .EpiTxDb as.list,EpiTxDb-method EpiTxDb EpiTxDb-class organism,EpiTxDb-method seqinfo,EpiTxDb-method seqlevels,EpiTxDb-method |
| EpiTxDb internal data | EpiTxDb-data rmbase_data |
| 'EpiTxDb' - Storing and accessing epitranscriptomic information using the AnnotationDbi interface | EpiTxDb-package#' |
| Creating a 'EpiTxDb' from user supplied annotations as 'data.frame's | makeEpiTxDb |
| Create a 'EpiTxDb' object from a 'GRanges' object | makeEpiTxDbFromGRanges |
| Create a 'EpiTxDb' object from RMBase v2.0 online resources | downloadRMBaseFiles EPITXDB_RMBASE_URL getRMBaseDataAsGRanges listAvailableGenomesFromRMBase listAvailableModFromRMBase listAvailableOrganismsFromRMBase makeEpiTxDbFromRMBase makeEpiTxDbFromRMBaseFiles |
| Create a 'EpiTxDb' object from tRNAdb resources | gettRNAdbDataAsGRanges listAvailableOrganismsFromtRNAdb makeEpiTxDbFromtRNAdb |
| Getting modification data from a 'EpiTxDb-object' | modifications modifications,EpiTxDb-method modificationsBy modificationsBy,EpiTxDb-method modifiedSeqsByTranscript modifiedSeqsByTranscript,EpiTxDb,DNAStringSet-method |
| Generate integer sequences from position information of 'Ranges' | as.integer,Ranges-method positionSequence positionSequence,Ranges-method positionSequence,RangesList-method |
| Rescaling 'Ranges' object | rescale rescale,GRanges-method rescale,GRangesList-method rescale,IRanges-method rescale,IRangesList-method |
| Using the "select" interface on 'EpiTxDb' objects | columns columns,EpiTxDb-method keys keys,EpiTxDb-method keytypes keytypes,EpiTxDb-method select select,EpiTxDb-method |
| Shift 'GRanges' coordinates based on another 'GRanges' object | shiftGenomicToTranscript shiftGenomicToTranscript,GRanges,GRangesList-method shiftGenomicToTranscript,GRangesList,GRangesList-method shiftTranscriptToGenomic shiftTranscriptToGenomic,GRanges,GRangesList-method shiftTranscriptToGenomic,GRangesList,GRangesList-method |
