User: josev.die

gravatar for josev.die
josev.die20
Reputation:
20
Status:
New User
Location:
Website:
https://jdieramon.gith...
Twitter:
jdieramon
Scholar ID:
Google Scholar Page
Last seen:
3 months, 1 week ago
Joined:
3 years, 5 months ago
Email:
j********@gmail.com

Posts by josev.die

<prev • 7 results • page 1 of 1 • next >
0
votes
4
answers
5.3k
views
4
answers
Answer: A: NCBI Protein GI to Genome Accession
... Using #R : # Dependencies library(rentrez) # NCBI Protein GI to Genome Accession gi = 817524604 gi_link = entrez_link(dbfrom = 'protein', db = 'nuccore', id = gi) nucc_id = gi_link$links$protein_nuccore nucc = entrez_summary(db = 'nuccore', id = nucc_id) nucc$c ...
written 3 months ago by josev.die20
1
vote
0
answers
4.7k
views
0
answers
Comment: C: How do I go from UniProt ID to retrieving the gene name?
... Using #R uniprot_mapping <- function(ids) { uri <- 'http://www.uniprot.org/uniprot/?query=' idStr <- paste(ids, collapse="+or+") format <- '&format=tab' fullUri <- paste0(uri,idStr,format) dat &l ...
written 7 months ago by josev.die20
0
votes
1
answer
981
views
1
answers
Answer: A: How do I make this perl script work to fetch sequences from NCBI using gene symb
... If you are open to use R, this code will do the work for you. #Dependency library(rentrez) #Loop over your gene symbols, fetch the protein sequence and put it into a fasta file save_AAfasta <- function(IDs, nameFile) { for(i in seq(length(IDs))) { myterm ...
written 16 months ago by josev.die20
0
votes
2
answers
989
views
2
answers
Answer: A: Unable to retrieve Fasta of certain NCBI entries given their accession number
... You can also use the following function written in R save_AAfasta <- function(xpsIds, nameFile) { for(i in seq(length(xpsIds))) { protein <- rentrez::entrez_summary(db = "protein", id = xpsIds[i]) protein_fasta <- rentrez::entrez_fetch(db="protein", id=protein$u ...
written 16 months ago by josev.die20
0
votes
1
answer
739
views
1
answers
Answer: A: Loading a genome in BSgenome
... Same question here. Please, let us know if you figure out how to do it. ...
written 2.8 years ago by josev.die20
0
votes
2
answers
1.4k
views
2
answers
Answer: A: Forge a BSgenome data package
... Your answer is exactly right. It is caused because I did not follow exactly the vignette (latest updated). There is no 'species' field for the description file. Concerning the incomplete line, I rebuilt the file and it worked. You likely have truncated your file in such a way that the final line is ...
written 3.1 years ago by josev.die20
2
votes
2
answers
1.4k
views
2
answers
Forge a BSgenome data package
... We work on the legume Chickpea which genome has been recently released but it does not have a BSgenome package so far. I though I'd try and make one. Following the vignette I have placed some FASTA chromosomes in a folder. I have started with a small example, so I have used just the first two chro ...
bsgenome seed file written 3.5 years ago by josev.die20

Latest awards to josev.die

Popular Question 16 months ago, created a question with more than 1,000 views. For Forge a BSgenome data package

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 773 users visited in the last hour