Package: ncRNAtools 1.23.2

Lara Selles Vidal

ncRNAtools: An R toolkit for non-coding RNA

ncRNAtools provides a set of basic tools for handling and analyzing non-coding RNAs. These include tools to access the RNAcentral database and to predict and visualize the secondary structure of non-coding RNAs. The package also provides tools to read, write and interconvert the file formats most commonly used for representing such secondary structures.

Authors:Lara Selles Vidal [cre, aut], Rafael Ayala [aut], Guy-Bart Stan [aut], Rodrigo Ledesma-Amaro [aut]

ncRNAtools_1.23.2.tar.gz
ncRNAtools_1.23.2.zip(r-4.7)ncRNAtools_1.23.2.zip(r-4.6)ncRNAtools_1.23.2.zip(r-4.5)
ncRNAtools_1.23.2.tgz(r-4.6-any)ncRNAtools_1.23.2.tgz(r-4.5-any)
ncRNAtools_1.23.2.tar.gz(r-4.7-any)ncRNAtools_1.23.2.tar.gz(r-4.6-any)
ncRNAtools_1.23.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ncRNAtools/json (API)
NEWS

# Install 'ncRNAtools' in R:

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

Bug tracker:https://github.com/larasellesvidal/ncrnatools/issues

On BioConductor:ncRNAtools-1.23.2(bioc 3.24)ncRNAtools-1.22.1(bioc 3.23)

functionalgenomics dataimport thirdpartyclient visualization structuralprediction

3.83 score 1 stars 34 scripts 350 downloads 15 exports 31 dependencies

Last updated from:b66e9bf6fe. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	153
linux-devel-x86_64	NOTE	199
source / vignettes	OK	230
linux-release-x86_64	NOTE	213
macos-release-arm64	NOTE	169
macos-oldrel-arm64	NOTE	144
windows-devel	NOTE	185
windows-release	NOTE	167
windows-oldrel	NOTE	179
wasm-release	OK	106

Exports:findPairedBases flattenDotBracket generatePairsProbabilityMatrix pairsToSecondaryStructure plotCompositePairsMatrix plotPairsProbabilityMatrix predictAlternativeSecondaryStructures predictSecondaryStructure readCT readDotBracket rnaCentralGenomicCoordinatesSearch rnaCentralRetrieveEntry rnaCentralTextSearch writeCT writeDotBracket

Dependencies:askpass BiocGenerics cli cpp11 curl farver generics GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lifecycle mime openssl R6 RColorBrewer rlang S4Vectors S7 scales Seqinfo sys vctrs viridisLite withr xml2

rfaRm

Rendered fromncRNAtools.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2026-04-30
Started: 2020-07-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Determines paired bases from secondary structure string	findPairedBases
Converts an extended Dot-Bracket secondary structure to basic Dot-Bracket notation	flattenDotBracket
Generates a matrix of base pair probabilities	generatePairsProbabilityMatrix
Generates a string with the secondary structure of an RNA sequence	pairsToSecondaryStructure
Plots a composite matrix of base pair probabilities and paired bases	plotCompositePairsMatrix
Plots a matrix of base pair probabilities	plotPairsProbabilityMatrix
Predicts alternative secondary structures of a given RNA sequence	predictAlternativeSecondaryStructures
Predicts the secondary structure of a given RNA sequence	predictSecondaryStructure
Reads a file with the secondary structure of an RNA in the CT format	readCT
Reads a file with the sequence and secondary structure of an RNA in the Dot-Bracket format	readDotBracket
Retrieves annotated non-coding RNA in a set of genomic ranges	rnaCentralGenomicCoordinatesSearch
Retrieves information for a specific entry of the RNAcentral database	rnaCentralRetrieveEntry
Searches the RNAcentral database with a text query	rnaCentralTextSearch
Writes a file with the secondary structure of an RNA in the CT format	writeCT
Writes a file with the sequence and secondary structure of an RNA in the Dot-Bracket format	writeDotBracket