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organism(<EpiTxDb>) seqinfo(<EpiTxDb>) seqlevels(<EpiTxDb>) as.list(<EpiTxDb>)
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EpiTxDb objects |
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rmbase_data
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EpiTxDb internal data |
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EpiTxDb-package#'
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EpiTxDb - Storing and accessing epitranscriptomic information
using the AnnotationDbi interface
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makeEpiTxDb()
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Creating a EpiTxDb from user supplied annotations as
data.frames |
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makeEpiTxDbFromGRanges()
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Create a EpiTxDb object from a GRanges object |
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EPITXDB_RMBASE_URL downloadRMBaseFiles() makeEpiTxDbFromRMBase() getRMBaseDataAsGRanges() makeEpiTxDbFromRMBaseFiles() listAvailableOrganismsFromRMBase() listAvailableGenomesFromRMBase() listAvailableModFromRMBase()
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Create a EpiTxDb object from RMBase v2.0 online resources |
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gettRNAdbDataAsGRanges() makeEpiTxDbFromtRNAdb() listAvailableOrganismsFromtRNAdb()
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Create a EpiTxDb object from tRNAdb resources |
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modifications() modificationsBy() modifiedSeqsByTranscript()
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Getting modification data from a EpiTxDb-object |
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positionSequence() as.integer(<Ranges>)
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Generate integer sequences from position information of Ranges |
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rescale()
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Rescaling Ranges object |
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select(<EpiTxDb>) columns(<EpiTxDb>) keys(<EpiTxDb>) keytypes(<EpiTxDb>)
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Using the "select" interface on EpiTxDb objects |
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shiftTranscriptToGenomic() shiftGenomicToTranscript()
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Shift GRanges coordinates based on another GRanges
object |