Package: refseqR 1.1.6

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_1.1.6.tar.gz
refseqR_1.1.6.zip(r-4.7)refseqR_1.1.6.zip(r-4.6)refseqR_1.1.6.zip(r-4.5)
refseqR_1.1.6.tgz(r-4.6-any)refseqR_1.1.6.tgz(r-4.5-any)
refseqR_1.1.6.tar.gz(r-4.7-any)refseqR_1.1.6.tar.gz(r-4.6-any)
refseqR_1.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
refseqR/json (API)

# Install 'refseqR' in R:

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

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

On CRAN:

4.30 score 4 stars 7 scripts 567 downloads 12 exports 28 dependencies

Last updated from:78b2470bf2. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	202
source / vignettes	OK	249
linux-release-x86_64	NOTE	160
macos-release-arm64	NOTE	200
macos-oldrel-arm64	NOTE	220
windows-devel	NOTE	117
windows-release	NOTE	113
windows-oldrel	NOTE	186
wasm-release	OK	109

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 generics glue httr IRanges jsonlite lifecycle magrittr mime openssl pillar pkgconfig R6 rentrez rlang S4Vectors Seqinfo sys tibble utf8 vctrs XML XVector

Working with the RefSeq database

0. Introduction | 1. Gene | 2. Transcript | 3. Protein | 4. Concluding Remarks

Rendered fromrefseqR.Rmdusingknitr::rmarkdown

Last update: 2024-12-25
Started: 2024-03-29

Citation

Development and contributors

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