Package: refseqR 1.1.4

Jose V. Die

refseqR: Common Computational Operations Working with RefSeq Entries (GenBank)

Fetches NCBI data (RefSeq <https://www.ncbi.nlm.nih.gov/refseq/> database) and provides an environment to extract information at the level of gene, mRNA or protein accessions.

Authors:Jose V. Die [aut, cre], Lluís Revilla Sancho [ctb]

refseqR_1.1.4.tar.gz
refseqR_1.1.4.tar.gz(r-4.5-noble)refseqR_1.1.4.tar.gz(r-4.4-noble)
refseqR_1.1.4.tgz(r-4.4-emscripten)refseqR_1.1.4.tgz(r-4.3-emscripten)
refseqR.pdf |refseqR.html✨
refseqR/json (API)

# Install 'refseqR' in R:

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

Bug tracker:https://github.com/jdieramon/refseqr/issues

12 exports 0.49 score 31 dependencies 4 scripts 550 downloads

Last updated 29 days agofrom:5400a25027. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 20 2024
R-4.5-linux	OK	Aug 20 2024

Exports:refseq_AAlen refseq_AAmol_wt refseq_AAseq refseq_CDScoords refseq_CDSseq refseq_description refseq_fromGene refseq_GeneID refseq_geneSymbol refseq_mRNAfeat refseq_protein2RNA refseq_RNA2protein

Dependencies:askpass BiocGenerics Biostrings cli crayon curl fansi GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite lifecycle magrittr mime openssl pillar pkgconfig R6 rentrez rlang S4Vectors sys tibble UCSC.utils utf8 vctrs XML XVector zlibbioc

Working with the RefSeq database

Rendered fromrefseqR.Rmdusingknitr::rmarkdownon Aug 20 2024.

Last update: 2024-08-19
Started: 2024-04-02

Citation

Readme and manuals

Help Manual

Help page	Topics
Get the amino acid length from a protein accession	refseq_AAlen
Get the amino acid length from a protein accession	refseq_AAlen_action
Extract the molecular weight from a protein accession	refseq_AAmol_wt
Extract the amino acid sequence into a Biostrings object	refseq_AAseq
Extract the coding sequences (CDS) coordinates from a transcript accession	refseq_CDScoords
Extract the CDS nucleotide sequence into a Biostrings object	refseq_CDSseq
Get the sequence Description	refseq_description
Get the mRNA or protein accession	refseq_fromGene
Get the mRNA or protein accession	refseq_fromGene_action
Get the GeneID	refseq_GeneID
Get the gene symbol	refseq_geneSymbol
Get the gene symbol	refseq_geneSymbol_action
Get mRNA features	refseq_mRNAfeat
Get the transcript accession from the protein accession	refseq_protein2RNA
Get the protein accession from the transcript accession	refseq_RNA2protein
refseqR: Common computational operations working with RefSeq	refseqR-package refseqR