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)
EpiTxDb_1.25.0.tgz(r-4.6-any)EpiTxDb_1.25.0.tgz(r-4.5-any)
EpiTxDb_1.25.0.tar.gz(r-4.7-any)EpiTxDb_1.25.0.tar.gz(r-4.6-any)
EpiTxDb_1.25.0.tgz(r-4.6-emscripten)
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:

rmbase_data - EpiTxDb internal data

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

software epitranscriptomics

3.52 score 11 scripts 525 downloads 28 exports 96 dependencies

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

Target	Result	Time
bioc-checks	ERROR	263
linux-devel	WARNING	488
source / vignettes	ERROR	392
linux-release	WARNING	485
macos-release	WARNING	363
macos-oldrel	WARNING	306
windows-devel	WARNING	387
windows-release	WARNING	322
windows-oldrel	WARNING	370
wasm-release	OK	195

Exports:as.list columns downloadRMBaseFiles EPITXDB_RMBASE_URL getRMBaseDataAsGRanges gettRNAdbDataAsGRanges keys keytypes listAvailableGenomesFromRMBase listAvailableModFromRMBase listAvailableOrganismsFromRMBase listAvailableOrganismsFromtRNAdb makeEpiTxDb makeEpiTxDbFromGRanges makeEpiTxDbFromRMBase makeEpiTxDbFromRMBaseFiles makeEpiTxDbFromtRNAdb modifications modificationsBy modifiedSeqsByTranscript organism positionSequence rescale select seqinfo seqlevels shiftGenomicToTranscript shiftTranscriptToGenomic

Dependencies:AnnotationDbi askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI dbplyr digest dplyr farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable hms httr httr2 IRanges isoband jsonlite KEGGREST labeling lambda.r lifecycle magrittr memoise mime Modstrings openssl pillar pkgconfig png prettyunits progress purrr R6 RColorBrewer RCurl restfulr rex Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Vectors S7 scales Seqinfo snow stringi stringr Structstrings sys tibble tidyr tidyselect tRNA tRNAdbImport txdbmaker UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

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