Package: refseqR 1.1.2
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:
refseqR_1.1.2.tar.gz
refseqR_1.1.2.zip(r-4.5)refseqR_1.1.2.zip(r-4.4)refseqR_1.1.2.zip(r-4.3)
refseqR_1.1.2.tgz(r-4.4-any)refseqR_1.1.2.tgz(r-4.3-any)
refseqR_1.1.2.tar.gz(r-4.5-noble)refseqR_1.1.2.tar.gz(r-4.4-noble)
refseqR_1.1.2.tgz(r-4.4-emscripten)refseqR_1.1.2.tgz(r-4.3-emscripten)
refseqR.pdf |refseqR.html✨
refseqR/json (API)
| # Install 'refseqR' in R: |
| install.packages('refseqR', repos = c('https://jdieramon.r-universe.dev', 'https://cloud.r-project.org')) |
The latest version of this package failed to build. Look at thebuild logs for more information.
Bug tracker:https://github.com/jdieramon/refseqr/issues
Last updated 3 months agofrom:3aa2898d21. Checks:OK: 1 ERROR: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 17 2024 |
| R-4.5-win | ERROR | Aug 17 2024 |
| R-4.5-linux | ERROR | Aug 17 2024 |
| R-4.4-win | ERROR | Aug 17 2024 |
| R-4.4-mac | ERROR | Aug 17 2024 |
| R-4.3-win | ERROR | Aug 17 2024 |
| R-4.3-mac | ERROR | Aug 17 2024 |
Exports:extract_from_xmrefseq_AA_lengthrefseq_AA_mol_wtrefseq_AAseqrefseq_CDScoordsrefseq_CDSseqrefseq_descriptionrefseq_fromGenerefseq_GeneIDrefseq_mRNA2proteinrefseq_mRNAfeatrefseq_protein2mRNA
Dependencies:askpassBiocGenericsBiostringsclicrayoncurlfansiGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rentrezrlangS4VectorssystibbleUCSC.utilsutf8vctrsXMLXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract some features from an XM accession | extract_from_xm |
| Get the amino acid length from a protein accession | refseq_AA_length |
| Extract the molecular weight from a protein accession | refseq_AA_mol_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 GeneID | refseq_GeneID |
| Get the gene symbol | refseq_geneSymbol |
| Get the protein accession from the transcript accession | refseq_mRNA2protein |
| Get mRNA features | refseq_mRNAfeat |
| Get the transcript accession from the protein accession | refseq_protein2mRNA |
| refseqR: Common computational operations working with RefSeq | refseqR-package refseqR |
