User: lizaveta

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lizaveta0
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Posts by lizaveta

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Comment: C: How To Update R In Ubuntu ?
... Worked 2019 April 17 ...
written 10 weeks ago by lizaveta0
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Comment: C: Different results from biomaRt query and search in GTF
... Thank you for the explanation! I believe, as I don't want to depend on external databases (I've been having a lot of trouble while looking for the coordinates of many genes via getBM due to ofter Ensembl mirrors shut-downs) I should use CDS + stop_codon mask from GTF file to get the same sets of co ...
written 3 months ago by lizaveta0
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Different results from biomaRt query and search in GTF
... I need all the exons coordinates for a specific gene transcript (let's say, "ENST00000269305"). I try to do it with 2 different methods: 1. using getBM from biomaRt library("biomaRt") human = useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",host="grch37.ensembl.org" ...
R biomart annotation transcripts hg19 written 3 months ago by lizaveta0 • updated 3 months ago by Emily_Ensembl18k
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GetBM gives controversial results
... I want to get chromosome location of SMARCA1 gene. library("biomaRt") human = useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",host="grch37.ensembl.org", path="/biomart/martservice") getBM(attributes = c("hgnc_symbol","chromosome_name", "start_position", ...
gene R bioconductor biomart written 9 months ago by lizaveta0

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