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diffBind
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2
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386
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
23 days ago • updated 22 days ago
Henry
▴ 10
2
votes
2
replies
171
views
[DiffBind] Obtaining normalization factors
DiffBind
22 days ago • updated 18 days ago
Henry
▴ 10
1
vote
1
reply
95
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
marcusn
• 0
0
votes
0
replies
34
views
dba.plotProfile() plotting and interpretation
DiffBind
1 day ago
Henry
▴ 10
0
votes
1
reply
127
views
ATACseq merge peaks
DiffBind
updated 8 days ago by
ATpoint
★ 4.1k • written 10 days ago by
Shloka
• 0
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
19 days ago
Virangika
• 0
0
votes
0
replies
31
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
2 days ago
Ian D.
▴ 70
0
votes
2
replies
112
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 2 days ago
Ian D.
▴ 70
0
votes
0
replies
38
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
2 days ago
yvonneh
• 0
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
17 days ago • updated 14 days ago
lonn
• 0
10 results • Page
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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