User: tangming2005

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tangming200590
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Posts by tangming2005

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Comment: C: claariom.s.human annotation error
... Thanks James. I upgraded R to the current. and somehow the old bioc packages are still linked to the new R version... The other way indeed worked. Best, Ming ...
written 7 months ago by tangming200590
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claariom.s.human annotation error
... code are below. Thank you! library(limma) library(oligo) library(pd.clariom.s.human) celFiles <- list.celfiles('.', full.names=TRUE) ab<- read.celfiles(celFiles) eset<- oligo::rma(ab) library("affycoretools") eset <- annotateEset(eset, annotation(eset)) Error: There appears to be ...
affcoretools pd.clariom.s.human written 7 months ago by tangming200590 • updated 7 months ago by James W. MacDonald46k
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Comment: C: unlist a exons GRangeslist object and add a gene name column
... good to know this! thanks. ...
written 7 months ago by tangming200590
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Comment: C: unlist a exons GRangeslist object and add a gene name column
... Thanks! How can I miss this function?!    If it is a list (not GRangesList) object, I would do  myname<- names(mylist) lapply(myname, function(x) mylist[[x]]$gene<- x) stack is very useful!   ...
written 7 months ago by tangming200590
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unlist a exons GRangeslist object and add a gene name column
... Hi, I can not find  a way to do it. exons <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene") unlist(exons) # this will lost the gene name information. How do I add the name of the gene for the exons? I have read https://www.biostars.org/p/101513/ and https://support.bioconductor.or ...
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene written 7 months ago by tangming200590 • updated 7 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Hi James, thanks very much for this detailed answer. now I remember a related question you answered me some time ago https://support.bioconductor.org/p/88725/#88767 again, your help is much appreciated. learned a lot! Tommy ...
written 8 months ago by tangming200590
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... thanks. looks like I can not find DAXX, HLA-A, SHOX and TRIM27 in TxDb.Hsapiens.UCSC.hg19.knownGene even using the other names. but POU5F1B is not shown either AnnotationDbi::select(org.Hs.eg.db, c("POU5F1", "DAXX", "HLA-A","SHOX","TRIM27"), keytype = "SYMBOL", columns = "ALIAS") 'select()' ret ...
written 8 months ago by tangming200590
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Thanks! I have a list of genes which I can not find in the txdb. DAXX, HLA-A, SHOX and TRIM27. where can I find the alternative names? Tommy   ...
written 8 months ago by tangming200590
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POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Hi, I was trying to get the coordinates of some genes, and was surprised that POU5F1 gene is not in the txdb. Thank you for looking into this. Tommy library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb<- TxDb.Hsapiens.UCSC.hg19.knownGene hg19.genes<- genes(txdb) library(AnnotationDbi) libra ...
txdb.hsapiens.ucsc.hg19.knowngene written 8 months ago by tangming200590 • updated 8 months ago by jma199130
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Comment: C: reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not s
... samtools view -F 256 will remove some reads, but not all not uniquely mapped reads. Have you tried TEQC on any BWA-MEM aligned bam files? from Heng Li: https://www.biostars.org/p/59281/#59303 Eland is probably the first short read aligner. It reports a tag, which can be '[UR][0-2]|NM', for each r ...
written 10 months ago by tangming200590

Latest awards to tangming2005

Great Question 13 months ago, created a question with more than 5,000 views. For DESeq2 for ChIP-seq differential peaks
Popular Question 13 months ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene
Popular Question 13 months ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Centurion 13 months ago, created 100 posts.
Popular Question 13 months ago, created a question with more than 1,000 views. For Gviz GeneRegionTrack draw only one gene in the range
Popular Question 13 months ago, created a question with more than 1,000 views. For How to bin a GRanges to small bins
Popular Question 2.2 years ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene
Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Supporter 2.2 years ago, voted at least 25 times.

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