Package: EpiTxDb 1.25.0

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:Felix G.M. Ernst [aut, cre]

EpiTxDb_1.25.0.tar.gz
EpiTxDb_1.25.0.zip(r-4.7-any)EpiTxDb_1.25.0.zip(r-4.6-any)EpiTxDb_1.25.0.zip(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EpiTxDb/json (API)

# 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

Datasets:

On BioConductor:EpiTxDb-1.25.0(bioc 3.24)EpiTxDb-1.24.0(bioc 3.23)

softwareepitranscriptomics

5.00 score 11 scripts 465 downloads 28 exports 95 dependencies

Last updated from:1bf0e24119. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR319
linux-develNOTE532
source / vignettesOK521
linux-releaseNOTE509
macos-releaseNOTE341
macos-oldrelNOTE400
windows-develNOTE426
windows-releaseNOTE423
windows-oldrelNOTE432
wasm-releaseOK254

Exports:as.listcolumnsdownloadRMBaseFilesEPITXDB_RMBASE_URLgetRMBaseDataAsGRangesgettRNAdbDataAsGRangeskeyskeytypeslistAvailableGenomesFromRMBaselistAvailableModFromRMBaselistAvailableOrganismsFromRMBaselistAvailableOrganismsFromtRNAdbmakeEpiTxDbmakeEpiTxDbFromGRangesmakeEpiTxDbFromRMBasemakeEpiTxDbFromRMBaseFilesmakeEpiTxDbFromtRNAdbmodificationsmodificationsBymodifiedSeqsByTranscriptorganismpositionSequencerescaleselectseqinfoseqlevelsshiftGenomicToTranscriptshiftTranscriptToGenomic

Dependencies:AnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrdplyrfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlifecyclemagrittrmemoisemimeModstringsopensslpillarpkgconfigpngprettyunitsprogresspurrrR6RColorBrewerRCurlrestfulrrexRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4VectorsS7scalesSeqinfosnowstringistringrStructstringssystibbletidyrtidyselecttRNAtRNAdbImporttxdbmakerUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryaml

EpiTxDb: creating an EpiTxDb object
Introduction | makeEpiTxDb and makeEpiTxDbFromGRanges | makeEpiTxDbFromtRNAdb | makeEpiTxDbFromRMBase | Session info | References
Rendered fromEpiTxDb-creation.Rmdusingknitr::rmarkdown

Last update: 2024-03-24
Started: 2020-02-26

EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface
Installation | Introduction | Getting started | Accessing RNA modifications | Shifting coordinates from genomic to transcriptomic | Session info | References
Rendered fromEpiTxDb.Rmdusingknitr::rmarkdown

Last update: 2021-03-25
Started: 2020-02-06

Readme and manuals

Help Manual

Help pageTopics
EpiTxDb objects.EpiTxDb as.list,EpiTxDb-method EpiTxDb EpiTxDb-class organism,EpiTxDb-method seqinfo,EpiTxDb-method seqlevels,EpiTxDb-method
EpiTxDb internal dataEpiTxDb-data rmbase_data
'EpiTxDb' - Storing and accessing epitranscriptomic information using the AnnotationDbi interfaceEpiTxDb-package#'
Creating a 'EpiTxDb' from user supplied annotations as 'data.frame'smakeEpiTxDb
Create a 'EpiTxDb' object from a 'GRanges' objectmakeEpiTxDbFromGRanges
Create a 'EpiTxDb' object from RMBase v2.0 online resourcesdownloadRMBaseFiles EPITXDB_RMBASE_URL getRMBaseDataAsGRanges listAvailableGenomesFromRMBase listAvailableModFromRMBase listAvailableOrganismsFromRMBase makeEpiTxDbFromRMBase makeEpiTxDbFromRMBaseFiles
Create a 'EpiTxDb' object from tRNAdb resourcesgettRNAdbDataAsGRanges 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' objectrescale rescale,GRanges-method rescale,GRangesList-method rescale,IRanges-method rescale,IRangesList-method
Using the "select" interface on 'EpiTxDb' objectscolumns columns,EpiTxDb-method keys keys,EpiTxDb-method keytypes keytypes,EpiTxDb-method select select,EpiTxDb-method
Shift 'GRanges' coordinates based on another 'GRanges' objectshiftGenomicToTranscript shiftGenomicToTranscript,GRanges,GRangesList-method shiftGenomicToTranscript,GRangesList,GRangesList-method shiftTranscriptToGenomic shiftTranscriptToGenomic,GRanges,GRangesList-method shiftTranscriptToGenomic,GRangesList,GRangesList-method