Package: tRNA 1.31.0

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_1.31.0.tar.gz
tRNA_1.31.0.zip(r-4.7)tRNA_1.31.0.zip(r-4.6)tRNA_1.31.0.zip(r-4.5)
tRNA_1.31.0.tgz(r-4.6-any)tRNA_1.31.0.tgz(r-4.5-any)
tRNA_1.31.0.tar.gz(r-4.7-any)tRNA_1.31.0.tar.gz(r-4.6-any)
tRNA_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tRNA/json (API)

# 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-1.31.0(bioc 3.24)tRNA-1.30.0(bioc 3.23)

software visualization bioconductor sequences structures trna

6.69 score 1 stars 3 packages 8 scripts 9 mentions 15 exports 31 dependencies

Last updated from:7d43907b84. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	189
linux-devel-x86_64	NOTE	339
source / vignettes	OK	341
linux-release-x86_64	NOTE	307
macos-release-arm64	NOTE	163
macos-oldrel-arm64	NOTE	221
windows-devel	NOTE	229
windows-release	NOTE	241
windows-oldrel	NOTE	226
wasm-release	OK	147

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

Dependencies:BiocGenerics Biostrings cli cpp11 crayon farver generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lifecycle magrittr Modstrings R6 RColorBrewer rlang S4Vectors S7 scales Seqinfo stringi stringr Structstrings vctrs viridisLite withr XVector

Analyzing tRNA sequences and structures

Rendered fromtRNA.Rmdusingknitr::rmarkdown

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