Package: rfaRm 1.25.1

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_1.25.1.tar.gz
rfaRm_1.25.1.zip(r-4.7)rfaRm_1.25.1.zip(r-4.6)rfaRm_1.25.1.zip(r-4.5)
rfaRm_1.25.1.tgz(r-4.6-any)rfaRm_1.25.1.tgz(r-4.5-any)
rfaRm_1.25.1.tar.gz(r-4.7-any)rfaRm_1.25.1.tar.gz(r-4.6-any)
rfaRm_1.25.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-1.25.0(bioc 3.24)rfaRm-1.23.0(bioc 3.23)

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

2.48 score 3 scripts 328 downloads 1 mentions 14 exports 35 dependencies

Last updated from:ac979b29fe. Checks:9 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	168
linux-devel-x86_64	ERROR	291
source / vignettes	ERROR	209
linux-release-x86_64	ERROR	426
macos-release-arm64	ERROR	175
macos-oldrel-arm64	ERROR	163
windows-devel	ERROR	165
windows-release	ERROR	211
windows-oldrel	ERROR	180
wasm-release	OK	125

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

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

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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

Package: rfaRm 1.25.1

rfaRm: An R interface to the Rfam database

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)