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DiffBind
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2
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335
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
7 days ago • updated 6 days ago
Henry
▴ 10
2
votes
2
replies
129
views
[DiffBind] Obtaining normalization factors
DiffBind
6 days ago • updated 2 days ago
Henry
▴ 10
0
votes
0
replies
89
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
20 days ago
Ankit
▴ 20
0
votes
0
replies
91
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
20 days ago
feather-W
• 0
0
votes
0
replies
54
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
3 days ago
Virangika
• 0
0
votes
1
reply
43
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 1 hour ago by
ATpoint
★ 4.0k • written 1 day ago by
lonn
• 0
0
votes
0
replies
117
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
29 days ago
erbrocato
• 0
0
votes
0
replies
77
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
21 days ago
Pierre Lindenbaum
▴ 10
8 results • Page
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Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
sredemption
• 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Answer: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
The genes are automatically ordered within `fgsea`, there is no need to sort them manually.
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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