Package: convertid 0.1.8

Vidal Fey

convertid: Convert Gene IDs Between Each Other and Fetch Annotations from Biomart

Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol() attempts to determine the most likely current Gene Symbol.

Authors:Vidal Fey [aut, cre], Henrik Edgren [aut]

convertid_0.1.8.tar.gz
convertid_0.1.8.tar.gz(r-4.5-noble)convertid_0.1.8.tar.gz(r-4.4-noble)
convertid_0.1.8.tgz(r-4.4-emscripten)convertid_0.1.8.tgz(r-4.3-emscripten)
convertid.pdf |convertid.html✨
convertid/json (API)

# Install 'convertid' in R:
install.packages('convertid', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

1.30 score 308 downloads 6 exports 67 dependencies

Last updated 12 months agofrom:5108d92079. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-linuxOKOct 25 2024

Exports:convert.aliasconvert.bmconvertId2get.bmlikely_symboltodisp2

Dependencies:AnnotationDbiaskpassassertthatBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdigestdplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslorg.Hs.eg.dborg.Mm.eg.dbpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRcpprlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrxml2XVectorzlibbioc