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DiffBind
•
reset
0
votes
0
replies
36
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
2 days ago
Dinesh
• 0
0
votes
0
replies
78
views
dba.plotProfile() plotting and interpretation
DiffBind
5 days ago
Henry
▴ 10
0
votes
0
replies
57
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
6 days ago
yvonneh
• 0
0
votes
0
replies
53
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
6 days ago
Ian D.
▴ 70
0
votes
3
replies
184
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 days ago • updated 1 day ago
Ian D.
▴ 70
1
vote
1
reply
128
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 8 days ago by
Michael Love
42k • written 8 days ago by
marcusn
• 0
0
votes
1
reply
141
views
ATACseq merge peaks
DiffBind
updated 12 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Shloka
• 0
0
votes
4
replies
244
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
21 days ago • updated 19 days ago
lonn
• 0
0
votes
0
replies
96
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
23 days ago
Virangika
• 0
2
votes
2
replies
173
views
[DiffBind] Obtaining normalization factors
DiffBind
26 days ago • updated 23 days ago
Henry
▴ 10
2
votes
2
replies
394
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
27 days ago • updated 26 days ago
Henry
▴ 10
0
votes
0
replies
115
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
5 weeks ago
feather-W
• 0
0
votes
0
replies
114
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
5 weeks ago
Ankit
▴ 20
0
votes
0
replies
102
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
6 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
144
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
7 weeks ago
erbrocato
• 0
0
votes
2
replies
255
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 weeks ago
Sam
▴ 10
0
votes
1
reply
202
views
Exact same results in Diffbind with different normalization methods
DiffBind
8 weeks ago • updated 7 weeks ago
red_bricks
▴ 50
0
votes
1
reply
307
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
251
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
179
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
173
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
0
votes
0
replies
246
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
4 months ago
Hai
• 0
0
votes
0
replies
262
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
1
vote
2
replies
333
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
0
votes
2
replies
360
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by
Sam
▴ 10
1
vote
1
reply
361
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
Miquel
• 0
0
votes
0
replies
337
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
412
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
sophie.hfliu
• 0
2
votes
2
replies
470
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 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 7 months ago by
Matt Eldridge
• 0 • written 7 months ago by
r.murakami
• 0
1
vote
1
reply
460
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
640
views
diffbind analyze for wheat
DiffBind
updated 10 weeks ago by
Igor
• 0 • written 7 months ago by
zgyu12
• 0
3
votes
7
replies
870
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 7 months ago by
Chris
• 0
0
votes
1
reply
554
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
943
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by
qq809825706
• 0 • written 8 months ago by
Mark
• 0
0
votes
2
replies
493
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
637
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago
Junsik
• 0
0
votes
3
replies
641
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
851
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
3.1k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
ANAMIKA
• 0
1
vote
1
reply
2.3k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
bhandary.8590
▴ 20
1
vote
4
replies
881
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 months ago • updated 9 months ago
Theo
▴ 10
1
vote
2
replies
692
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 10 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 10 months ago by
Chris
• 0
2
votes
3
replies
627
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by
meghanapple2
• 0 • written 10 months ago by
Chris
• 0
4
votes
4
replies
828
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
1
vote
2
replies
786
views
Interpret plots from DiffBind
DiffBind
11 months ago • updated 10 months ago
Chris
• 0
0
votes
1
reply
552
views
DiffBind output issues
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
David.Atkinson2
• 0
0
votes
0
replies
436
views
Help with error running DiffBind
DiffBind
11 months ago
Chris
• 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by
James W. MacDonald
65k • written 11 months ago by
kyliecode
• 0
50 results • Page
1 of 1
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Comment: deseq2 results
by
sajadahmad41454
• 0
could you please tell me if the results are fine or not? ![pca summary][1] ![pca plot][2] [1]: /media/images/ee7d8693-bcbe-4a7a-a566-d3…
Answer: normalization using Deseq2
by
ATpoint
★ 4.1k
counts(dds, normalized=TRUE)
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I have tried what you suggested. I started with methylation loci. I created segment1 and segment2 but how to combine them bec…
Comment: EGSEA usage with microarray data (with vooma)?
by
Chris
• 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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