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DEseq2
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DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 22 hours ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
33
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
21 hours ago
quanah.hudson
• 0
0
votes
0
replies
19
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
20 hours ago
lonn
• 0
0
votes
0
replies
27
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
20 hours ago • updated 18 hours ago
ussarizona
• 0
0
votes
0
replies
5
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
1 hour ago
09191919
• 0
0
votes
2
replies
260
views
DESeq filtering specific to contrasts
DESeq2
updated 57 minutes ago by
Carlin95
• 0 • written 8 weeks ago by
Emma
• 0
0
votes
0
replies
3
views
rlog transformation
DESeq2
20 minutes ago
ishij9717
• 0
7 results • Page
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Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark
by
jacques.imbert
• 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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