Package: rfaRm 1.19.0

Lara Selles Vidal

rfaRm: An R interface to the Rfam database

rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.

Authors:Lara Selles Vidal, Rafael Ayala, Guy-Bart Stan, Rodrigo Ledesma-Amaro

rfaRm_1.19.0.tar.gz
rfaRm_1.19.0.zip(r-4.5)rfaRm_1.19.0.zip(r-4.4)rfaRm_1.19.0.zip(r-4.3)
rfaRm_1.19.0.tgz(r-4.4-any)rfaRm_1.19.0.tgz(r-4.3-any)
rfaRm_1.19.0.tar.gz(r-4.5-noble)rfaRm_1.19.0.tar.gz(r-4.4-noble)
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rfaRm.pdf |rfaRm.html✨
rfaRm/json (API)
NEWS

# Install 'rfaRm' in R:

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

On BioConductor:rfaRm-1.19.0(bioc 3.21)rfaRm-1.18.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

functionalgenomics dataimport thirdpartyclient visualization multiplesequencealignment

3.60 score 1 scripts 154 downloads 1 mentions 14 exports 39 dependencies

Last updated 25 days agofrom:7c62429965. Checks:OK: 1 ERROR: 3 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	WARNING	Nov 19 2024
R-4.5-linux	ERROR	Nov 19 2024
R-4.4-win	WARNING	Nov 19 2024
R-4.4-mac	ERROR	Nov 19 2024
R-4.3-win	WARNING	Nov 19 2024
R-4.3-mac	ERROR	Nov 19 2024

Exports:rfamConsensusSecondaryStructure rfamCovarianceModel rfamFamilyAccessionToID rfamFamilyIDToAccession rfamFamilySummary rfamPDBMapping rfamSecondaryStructurePlot rfamSecondaryStructureXMLSVG rfamSeedAlignment rfamSeedTree rfamSeedTreeImage rfamSequenceRegions rfamSequenceSearch rfamTextSearchFamilyAccession

Dependencies:askpass BiocGenerics Biostrings cli crayon curl data.table fansi generics GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite lifecycle magick magrittr mime openssl pillar pkgconfig R6 Rcpp rlang rsvg rvest S4Vectors selectr stringi stringr sys tibble UCSC.utils utf8 vctrs xml2 XVector zlibbioc

rfaRm

Rendered fromrfaRm.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2020-04-08
Started: 2020-04-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Retrieve the secondary structure of an Rfam family	rfamConsensusSecondaryStructure
Get the covariance model associated to an Rfam family	rfamCovarianceModel
Convert an Rfam family accession to an Rfam family ID	rfamFamilyAccessionToID
Convert an Rfam family ID to an Rfam family accession	rfamFamilyIDToAccession
Get a summary describing an Rfam family	rfamFamilySummary
Retrieve PDB entries with the 3D structure of members of an Rfam family	rfamPDBMapping
Generate a diagram of the secondary structure of an Rfam family	rfamSecondaryStructurePlot
Get an SVG file with a secondary structure representation of an Rfam family	rfamSecondaryStructureXMLSVG
Retrieve the seed alignment of an Rfam family	rfamSeedAlignment
Get the phylogenetic tree of the seed multiple alignment of an Rfam family	rfamSeedTree
Get an image of the phylogenetic tree of the seed multiple alignment of an Rfam family	rfamSeedTreeImage
Retrieve all sequence regions belonging to an Rfam family	rfamSequenceRegions
Performs a sequence search of the Rfam database	rfamSequenceSearch
Search the Rfam database by a given keyword	rfamTextSearchFamilyAccession