User: tangming2005

gravatar for tangming2005
tangming2005150
Reputation:
150
Status:
Trusted
Location:
United States
Last seen:
4 months, 3 weeks ago
Joined:
5 years, 2 months ago
Email:
t***********@gmail.com

Posts by tangming2005

<prev • 118 results • page 1 of 12 • next >
0
votes
0
answers
156
views
0
answers
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 7 months ago by tangming2005150
0
votes
0
answers
156
views
0
answers
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 7 months ago by tangming2005150
0
votes
0
answers
156
views
0
answers
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 7 months ago by tangming2005150
0
votes
1
answer
219
views
1
answers
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 12 months ago by tangming2005150
0
votes
2
answers
2.3k
views
2
answers
Comment: C: DiffBind differential binding normalization with different levels of binding
... Thanks! this helps me a lot. ...
written 15 months ago by tangming2005150
0
votes
2
answers
2.3k
views
2
answers
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 16 months ago by tangming2005150
0
votes
1
answer
1.1k
views
1
answers
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 2.1 years ago by tangming2005150
2
votes
1
answer
1.1k
views
1
answer
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 2.1 years ago by tangming2005150 • updated 2.1 years ago by James W. MacDonald52k
0
votes
2
answers
633
views
2
answers
Comment: C: unlist a exons GRangeslist object and add a gene name column
... good to know this! thanks. ...
written 2.1 years ago by tangming2005150
0
votes
2
answers
633
views
2
answers
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 2.1 years ago by tangming2005150

Latest awards to tangming2005

Popular Question 11 months ago, created a question with more than 1,000 views. For TxDb.Hsapiens.UCSC.hg19.knownGene misannotation of a gene
Great Question 12 months ago, created a question with more than 5,000 views. For annotate GRanges with upstream or downstream nearest gene
Popular Question 19 months ago, created a question with more than 1,000 views. For IdeogramTrack from Gviz with chromosome name "4" rather "chr4"
Great Question 2.5 years ago, created a question with more than 5,000 views. For DESeq2 for ChIP-seq differential peaks
Centurion 2.5 years ago, created 100 posts.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Gviz GeneRegionTrack draw only one gene in the range
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to bin a GRanges to small bins
Popular Question 2.5 years ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Supporter 3.6 years ago, voted at least 25 times.
Popular Question 3.6 years ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Popular Question 3.6 years ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 340 users visited in the last hour