User: spromanos

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spromanos0
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USA/Boston/Dana-Farber Cancer Institute, Broad Institute
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7 months, 3 weeks ago
Joined:
9 months, 1 week ago
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r*****@hotmail.com

Posts by spromanos

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Package SomaticCancerAlterations, import own .maf file?
... Hi Julian,  I want to use SomaticSignatures on a maf file and I am dealing with the same issue. I loaded SomaticCancerAlterations and tried converting to a GRanges object, however I bumped into this error message:  all.gr <- SomaticCancerAlterations:::.maf2gr("all.maf") Error in maf$Chromosome ...
written 8 months ago by spromanos0
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Comment: C: Error in tximport, unused argument (reader = read_tsv)
... It seems like reader argument has been replaced with importer. This works just fine: txi.rsem <- tximport(files, type = "rsem", importer = read_tsv) ...
written 8 months ago by spromanos0
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Error in tximport, unused argument (reader = read_tsv)
... Hello, I tried to re-run the same script on the same samples and I encountered this error.  txi.rsem <- tximport(files, type = "rsem", reader = read_tsv) Error in tximport(files, type = "rsem", reader = read_tsv) : unused argument (reader = read_tsv) The only thing that changed between t ...
deseq2 tximport written 8 months ago by spromanos0 • updated 8 months ago by Michael Love18k
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Comment: C: Biomart ensembl annotation does not completely match my gene names
... Hi Herve,  I have made some progress, but there are still missing genes. I am using DESeq2 for DE analysis and a tab delimited file a bioinformatician shared with me containing ensembl gene IDs and HUGO symbols. I have since asked them where the file originated from, as I do find discrepancies; ma ...
written 9 months ago by spromanos0
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Biomart ensembl annotation does not completely match my gene names
... I am using getBM to get start/end positions for my genes, however biomart ensembl hgnz_names only contain 19869 out of my 29581 genes. In my dataset, gene names are HUGO, too. It seems that around 10,000 of my genes are not included in the total of 36,713 genes in biomart ensembl. I checked to see i ...
biomart ensemblbiomart written 9 months ago by spromanos0 • updated 9 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: KaryoploteR does not work on R.3.3.3
... Thanks so much! ...
written 9 months ago by spromanos0
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KaryoploteR does not work on R.3.3.3
... Although on the bioconductor page of KaryoploteR it states that it is compatible with 3.3 R versions, it is not available for 3.3.3. Which version should I download for it to work? Thanks! ...
karyoploter written 9 months ago by spromanos0 • updated 9 months ago by bgel10

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