Package: tRNA 1.25.0

Felix GM Ernst

tRNA: Analyzing tRNA sequences and structures

The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets.

Authors:Felix GM Ernst [aut, cre]

tRNA_1.25.0.tar.gz
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tRNA.pdf |tRNA.html✨
tRNA/json (API)
NEWS

# Install 'tRNA' in R:

install.packages('tRNA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/felixernst/trna/issues

Datasets:

gr - TRNA example data
gr_eco - TRNA example data
gr_human - TRNA example data
gr_human2 - TRNA example data

On BioConductor:tRNA-1.25.0(bioc 3.21)tRNA-1.24.0(bioc 3.20)

software visualization bioconductor sequences structures trna

6.91 score 1 stars 3 packages 3 scripts 348 downloads 9 mentions 15 exports 51 dependencies

Last updated 2 months agofrom:41b4ba97da. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 26 2024
R-4.5-win	NOTE	Nov 26 2024
R-4.5-linux	NOTE	Nov 26 2024
R-4.4-win	NOTE	Nov 26 2024
R-4.4-mac	NOTE	Nov 26 2024
R-4.3-win	NOTE	Nov 26 2024
R-4.3-mac	NOTE	Nov 26 2024

Exports:gettRNABasePairing gettRNAFeaturePlots gettRNALoopIDs gettRNAstructureGRanges gettRNAstructureSeqs gettRNASummary hasAcceptorStem hasAnticodonLoop hasAnticodonStem hasDloop hasDStem hasTloop hasTStem hasVariableLoop istRNAGRanges

Dependencies:askpass BiocGenerics Biostrings cli colorspace crayon curl fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv mime Modstrings munsell nlme openssl pillar pkgconfig R6 RColorBrewer rlang S4Vectors scales stringi stringr Structstrings sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Analyzing tRNA sequences and structures

Felix G.M. Ernst

Rendered fromtRNA.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2020-01-21
Started: 2018-09-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Accessing Dot Bracket annotation of tRNAs	gettRNABasePairing gettRNABasePairing,GRanges-method gettRNALoopIDs gettRNALoopIDs,GRanges-method
Graphical summary of tRNA features	gettRNAFeaturePlots gettRNAFeaturePlots,GRangesList-method
tRNA structures and sequences	gettRNAstructureGRanges gettRNAstructureGRanges,GRanges-method gettRNAstructureSeqs gettRNAstructureSeqs,GRanges-method
Summary of tRNA features	gettRNASummary gettRNASummary,GRanges-method gettRNASummary,GRangesList-method
Subsetting tRNAs	hasAcceptorStem hasAcceptorStem,GRanges-method hasAnticodonLoop hasAnticodonLoop,GRanges-method hasAnticodonStem hasAnticodonStem,GRanges-method hasDloop hasDloop,GRanges-method hasDStem hasDStem,GRanges-method hasTloop hasTloop,GRanges-method hasTStem hasTStem,GRanges-method hasVariableLoop hasVariableLoop,GRanges-method tRNA-subset
tRNA compatibility check	istRNAGRanges istRNAGRanges,GRanges-method
tRNA: analyzing tRNA sequences and structures	tRNA-package tRNA
tRNA example data	gr gr_eco gr_human gr_human2 tRNA-data