User: foehn

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foehn60
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Posts by foehn

<prev • 37 results • page 1 of 4 • next >
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biomaRt fails to retrieve GO description for some particular gene
... Hello, I'm having trouble finding GO terms and definitions for a list of genes using biomaRt. The problem seems to be specific to some genes instead of all. For exmaple, > library("tibble") > library("biomaRt") > BM = useMart("ensembl", dataset = "hsapiens_gene_ensembl") ...
go biomart R bioconductor symbol written 3 months ago by foehn60
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Comment: C: biomaRt Ensembl gene ID to multiple HGNC symbol
... According to Ensembl's reply, they arbitrarily pick a HGNC synonym for the summary if multiple. ...
written 7 months ago by foehn60
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Comment: C: biomaRt Ensembl gene ID to multiple HGNC symbol
... Good idea. ...
written 7 months ago by foehn60
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Comment: C: biomaRt Ensembl gene ID to multiple HGNC symbol
... Right. But I'm curious about why http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230417;r=10:78179185-78551355 returns LINC00856 as the Name in Summary section. Does it imply that Ensembl regards LINC00856 as a more canonical symbol than the other? ...
written 7 months ago by foehn60
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biomaRt Ensembl gene ID to multiple HGNC symbol
... Hi, I'm using R package `biomaRt` to map Ensembl gene IDs to HGNC symbols. I find some Ensembl IDs can be mapped to multiple symbols. For example, ``` mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = "ensembl_gene_id", ...
biomart ensembl symbol hgnc written 7 months ago by foehn60 • updated 7 months ago by James W. MacDonald52k
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Comment: C: biomaRt returns all NAs for hgnc_symbol
... Thanks to the detailed answer. Understood what you and @swbarnes2 mean. But it's a bit weird that the same code worked years ago... ...
written 7 months ago by foehn60
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Comment: C: biomaRt returns all NAs for hgnc_symbol
... `sumis.na` should be `sum(is.na`, and same for `allis.na` and `anyis.na`. Don't know why they are shown differently from the preview... ...
written 7 months ago by foehn60
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biomaRt returns all NAs for hgnc_symbol
... Hello, I'm trying to map mouse symbols to human, using R package `biomaRt`. Here is my code. ``` bm <- useMart(biomart = 'ensembl', dataset = "mmusculus_gene_ensembl") > SymbolMap <- getBM(attributes = c("mgi_symbol", "hgnc_symbol", "ensembl_gene_id"), filters = "mgi_symbol", mart = bm, ...
biomart written 7 months ago by foehn60 • updated 7 months ago by Mike Smith4.0k
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Comment: C: How to tell a GAlignmentsList singleton is mate1 or mate2
... Nice! thanks to both. ...
written 8 months ago by foehn60
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How to tell a GAlignmentsList singleton is mate1 or mate2
... Hello, I'm using `readGAlignmentsList` from package "GenomicAlignments" to read a paired-end sequencing BAM file, which contains both paired mates and singleton reads (R1 or R2 unmapped). According to the manual, "readGAlignmentsList pairs records into mates according to the pairing criteria des ...
rsamtools genomicalignments galignmentslist written 8 months ago by foehn60 • updated 8 months ago by James W. MacDonald52k

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Supporter 10 months ago, voted at least 25 times.

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