I have a list of accession numbers about 5000plus. I want to pull down the protein names for this list of ids, I have.
Can someone guide how can I do it using R programming ?
Dear Alok Patra
These links might be helpful, have a look:
1. https://cran.r-project.org/web/packages/UniprotR/UniprotR.pdf
2. https://www.biostars.org/p/432321/
3. https://www.ncbi.nlm.nih.gov/guide/howto/dwn-records/
Kind Regards
Qamar Ul Islam
As mentioned by Qamar Ul Islam , I suggest using the UniprotR package and its function GetNamesTaxa().
Best wishes,
Francesco
Try Biomartr
# Install core Bioconductor packages if (!requireNamespace("BiocManager")) install.packages("BiocManager") BiocManager::install()
# Install package dependencies BiocManager::install("Biostrings", version = "3.8") BiocManager::install("biomaRt", version = "3.8")
# install biomartr 0.9.0 install.packages("biomartr", dependencies = TRUE)
#example 1 from NCBI
HS.proteome.genbank
Dear Francesco Sanmarchi
Thank you for your appreciation and recommendation.
Stay Happy Stay Healthy.
Thank you all for the suggestions. Appreciate your timely help.
I managed to use, BiomaRt, Bioconductor R package.
Reference link:
https://m.ensembl.org/info/data/biomart/biomart_r_package.html
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