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Diffbind
•
reset
0
votes
1
reply
51
views
ATACseq merge peaks
DiffBind
updated 10 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
Shloka
• 0
0
votes
4
replies
200
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
9 days ago • updated 6 days ago
lonn
• 0
0
votes
0
replies
78
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
11 days ago
Virangika
• 0
2
votes
2
replies
150
views
[DiffBind] Obtaining normalization factors
DiffBind
14 days ago • updated 10 days ago
Henry
▴ 10
2
votes
2
replies
362
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
15 days ago • updated 14 days ago
Henry
▴ 10
0
votes
0
replies
99
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
28 days ago
feather-W
• 0
0
votes
0
replies
99
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
28 days ago
Ankit
▴ 20
0
votes
0
replies
84
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
29 days ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
126
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
5 weeks ago
erbrocato
• 0
0
votes
2
replies
230
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago
Sam
▴ 10
0
votes
1
reply
188
views
Exact same results in Diffbind with different normalization methods
DiffBind
6 weeks ago • updated 5 weeks ago
red_bricks
▴ 50
0
votes
1
reply
290
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
3 months ago
isaromero8888
• 0
0
votes
0
replies
235
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
3 months ago
Jawahar
• 0
0
votes
0
replies
168
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
160
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
0
votes
0
replies
228
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
3 months ago
Hai
• 0
0
votes
0
replies
247
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
3 months ago
inna.gur
• 0
1
vote
2
replies
320
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
0
votes
2
replies
337
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by
Sam
▴ 10
1
vote
1
reply
343
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
Miquel
• 0
0
votes
0
replies
322
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
5 months ago
jared.andrews07
▴ 30
0
votes
0
replies
394
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
sophie.hfliu
• 0
2
votes
2
replies
456
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago
r.murakami
• 0
2
votes
4
replies
1.2k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 6 months ago by
Matt Eldridge
• 0 • written 6 months ago by
r.murakami
• 0
1
vote
1
reply
439
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
lin.pei26
• 0
0
votes
3
replies
616
views
diffbind analyze for wheat
DiffBind
updated 8 weeks ago by
Igor
• 0 • written 7 months ago by
zgyu12
• 0
3
votes
7
replies
847
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 7 months ago by
Chris
• 0
0
votes
1
reply
533
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago
Mark
• 0
0
votes
1
reply
920
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by
qq809825706
• 0 • written 8 months ago by
Mark
• 0
0
votes
2
replies
459
views
DiffBind error
DiffBind
updated 8 months ago by
Rory Stark
★ 5.2k • written 8 months ago by
M.Vukic
• 0
1
vote
2
replies
602
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago
Junsik
• 0
0
votes
3
replies
612
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
jason.kost
• 0
0
votes
2
replies
804
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 9 months ago by
Malcolm Cook
★ 1.6k • written 9 months ago by
Nebat
• 0
0
votes
5
replies
3.0k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
ANAMIKA
• 0
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
bhandary.8590
▴ 20
1
vote
4
replies
844
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago
Theo
▴ 10
1
vote
2
replies
667
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
Stevie Pederson
• 0
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
Chris
• 0
2
votes
3
replies
602
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by
meghanapple2
• 0 • written 10 months ago by
Chris
• 0
4
votes
4
replies
795
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
1
vote
2
replies
758
views
Interpret plots from DiffBind
DiffBind
10 months ago
Chris
• 0
0
votes
1
reply
537
views
DiffBind output issues
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
David.Atkinson2
• 0
0
votes
0
replies
421
views
Help with error running DiffBind
DiffBind
10 months ago
Chris
• 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 4 months ago by
James W. MacDonald
65k • written 10 months ago by
kyliecode
• 0
0
votes
0
replies
403
views
Title in dba.plotProfile
DiffBind
11 months ago
agata17
• 0
8
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
Chris
• 0
1
vote
4
replies
998
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
lin.pei26
• 0
1
vote
0
replies
552
views
Fold values in Diffbind
DiffBind
11 months ago
bhandary.8590
▴ 20
0
votes
1
reply
651
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
Shashank
• 0
2
votes
3
replies
778
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 11 months ago by
jandrade
• 0
50 results • Page
1 of 1
Recent ...
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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