User: tangming2005

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tangming2005140
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4 years, 9 months ago
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Posts by tangming2005

<prev • 118 results • page 1 of 12 • next >
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Comment: C: calculating TSS enrichment from ATACseq data
... genomation has some functions https://bioconductor.org/packages/devel/bioc/vignettes/genomation/inst/doc/GenomationManual.html I am reading the source code. Thanks. ...
written 5 weeks ago by tangming2005140
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Comment: C: calculating TSS enrichment from ATACseq data
... or if there is any package there for this purpose, I want to take a look at the source code and learn. ...
written 5 weeks ago by tangming2005140
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calculating TSS enrichment from ATACseq data
... How to calculate the TSS enrichment score according to the ENCODE standard https://www.encodeproject.org/data-standards/terms/#enrichment? I was reading the source code https://github.com/jianhong/ATACseqQC/blob/master/R/TSSEscore.R#L80 but think it is not doing it correctly. library(TxDb.Hsa ...
genomicranges views tss atacseq written 5 weeks ago by tangming2005140
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Comment: C: DiffBind Change of Metadata once dba.counts have been called
... after I change the meta data  myDBA$class[DBA_TISSUE, ]<- myvector myDBA$masks is not showing the changed meta data Thanks! ...
written 6 months ago by tangming2005140
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Comment: C: DiffBind differential binding normalization with different levels of binding
... Thanks! this helps me a lot. ...
written 10 months ago by tangming2005140
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Comment: C: DiffBind differential binding normalization with different levels of binding
... Hi Rory, a related question.  I am using diffbind for H3K36me3 in 2 control vs 2 KO. we expect to see global H3K36me3 in KO samples. because H3K36me3 is enriched in the gene body (peak calling does not work well for those diffused marks). I use the gene body as the peak regions for all samples. I w ...
written 10 months ago by tangming2005140
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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 19 months ago by tangming2005140
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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 19 months ago by tangming2005140 • updated 19 months ago by James W. MacDonald50k
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Comment: C: unlist a exons GRangeslist object and add a gene name column
... good to know this! thanks. ...
written 19 months ago by tangming2005140
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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 19 months ago by tangming2005140

Latest awards to tangming2005

Great Question 6 months ago, created a question with more than 5,000 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 IdeogramTrack from Gviz with chromosome name "4" rather "chr4"
Centurion 2.1 years ago, created 100 posts.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Gviz GeneRegionTrack draw only one gene in the range
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to bin a GRanges to small bins
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Great Question 2.1 years ago, created a question with more than 5,000 views. For DESeq2 for ChIP-seq differential peaks
Popular Question 2.1 years ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene
Supporter 3.2 years ago, voted at least 25 times.
Popular Question 3.2 years ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Popular Question 3.2 years ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene

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