User: foehn

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foehn60
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Posts by foehn

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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 10 weeks ago by foehn60
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Comment: C: biomaRt Ensembl gene ID to multiple HGNC symbol
... Good idea. ...
written 10 weeks 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 10 weeks 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 10 weeks ago by foehn60 • updated 10 weeks ago by James W. MacDonald50k
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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 12 weeks 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 12 weeks 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 12 weeks ago by foehn60 • updated 12 weeks ago by Mike Smith3.8k
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Comment: C: How to tell a GAlignmentsList singleton is mate1 or mate2
... Nice! thanks to both. ...
written 3 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 3 months ago by foehn60 • updated 3 months ago by James W. MacDonald50k
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Comment: C: How to set track attributes in rtracklayer
... v1.42.2 works now. ...
written 4 months ago by foehn60

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Supporter 6 months ago, voted at least 25 times.

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