Package: ncRNAtools 1.17.0

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_1.17.0.tar.gz
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ncRNAtools.pdf |ncRNAtools.html✨
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-1.17.0(bioc 3.21)ncRNAtools-1.16.0(bioc 3.20)

functionalgenomics dataimport thirdpartyclient visualization structuralprediction

3.38 score 1 stars 12 scripts 154 downloads 15 exports 46 dependencies

Last updated 23 days agofrom:d839ffb5b3. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	WARNING	Nov 18 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Nov 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Nov 18 2024

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

Dependencies:askpass BiocGenerics cli colorspace curl fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer rlang S4Vectors scales sys tibble UCSC.utils utf8 vctrs viridisLite withr xml2 XVector zlibbioc

rfaRm

Rendered fromncRNAtools.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2020-09-07
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