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peaks
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3
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4.0k
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Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind
chipseq
peaks
dba
is.na
6.0 years ago
maria.kondili
▴ 10
2
votes
3
replies
2.3k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind
chipseq
counts
peaks
bedtools
updated 3.0 years ago by
Rory Stark
★ 5.1k • written 6.0 years ago by
Ni-Ar
▴ 10
1
vote
1
reply
1.4k
views
How do I know which peak to analyze?
bioconductor
annotation
peaks
updated 6.4 years ago by
Sean Davis
21k • written 6.4 years ago by
schaud24
▴ 10
0
votes
0
replies
739
views
Are broad/narrow peak comparable?
Peaks
MAC2
DiffBind
2.8 years ago
Yuan Tian
▴ 270
0
votes
4
replies
948
views
nucleR ERROR unable to find an inherited method for function peakDetection for signature
nucleosome
peaks
error
Job
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
anne.kannengiesser
• 0
5 results • Page
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Comment: Finding DEGs by using edgeR
by
Gordon Smyth
50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
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A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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