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Showing :
DiFFBind
•
reset
0
votes
0
replies
38
views
Difference in Contrast in DiffBind
DiffBind
4 days ago
zzrammal
• 0
0
votes
0
replies
93
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
12 days ago
Dinesh
• 0
0
votes
0
replies
120
views
dba.plotProfile() plotting and interpretation
DiffBind
15 days ago
Henry
▴ 10
0
votes
0
replies
92
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
17 days ago
yvonneh
• 0
0
votes
0
replies
87
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
17 days ago
Ian D.
▴ 70
0
votes
4
replies
375
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 7 days ago by
Ziliang
• 0 • written 18 days ago by
Ian D.
▴ 70
1
vote
1
reply
157
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
marcusn
• 0
0
votes
1
reply
171
views
ATACseq merge peaks
DiffBind
updated 23 days ago by
ATpoint
★ 4.1k • written 24 days ago by
Shloka
• 0
0
votes
4
replies
269
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 29 days ago
lonn
• 0
0
votes
0
replies
107
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 weeks ago
Virangika
• 0
2
votes
2
replies
191
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
2
votes
2
replies
417
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 weeks ago
Henry
▴ 10
0
votes
0
replies
126
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
7 weeks ago
feather-W
• 0
0
votes
0
replies
124
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
7 weeks ago
Ankit
▴ 20
0
votes
0
replies
111
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
7 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
150
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 weeks ago
erbrocato
• 0
0
votes
2
replies
275
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago
Sam
▴ 10
0
votes
1
reply
215
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago
red_bricks
▴ 50
0
votes
1
reply
327
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
268
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
193
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
4 months ago
frueher
• 0
0
votes
0
replies
184
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
4 months ago
Aswathy
• 0
0
votes
0
replies
270
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
4 months ago
Hai
• 0
0
votes
0
replies
282
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
0
votes
1
reply
958
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
379
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by
Sam
▴ 10
1
vote
2
replies
351
views
Inconsistent results in DiffBind
DiffBind
5 months ago
Sam
▴ 10
1
vote
1
reply
377
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
351
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
6 months ago
jared.andrews07
▴ 30
0
votes
0
replies
429
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
4
replies
1.3k
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
2
votes
2
replies
486
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago
r.murakami
• 0
1
vote
1
reply
472
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
3
votes
7
replies
884
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 8 months ago by
Chris
▴ 10
0
votes
3
replies
657
views
diffbind analyze for wheat
DiffBind
updated 11 weeks ago by
Igor
• 0 • written 8 months ago by
zgyu12
• 0
0
votes
1
reply
569
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago
Mark
• 0
1
vote
2
replies
658
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
2
replies
510
views
DiffBind error
DiffBind
updated 8 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
M.Vukic
• 0
0
votes
2
replies
879
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
1
vote
1
reply
2.0k
views
Help with error DiffBind
DiffBind
updated 9 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
Chris
▴ 10
1
vote
1
reply
2.4k
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
0
votes
5
replies
3.2k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
ANAMIKA
• 0
0
votes
3
replies
675
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
5
replies
1.2k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by
Rory Stark
★ 5.2k • written 4.3 years ago by
Jim
• 0
1
vote
4
replies
908
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 months ago
Theo
▴ 10
1
vote
2
replies
712
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
0
votes
1
reply
564
views
DiffBind output issues
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
David.Atkinson2
• 0
1
vote
2
replies
828
views
Interpret plots from DiffBind
DiffBind
11 months ago • updated 10 months ago
Chris
▴ 10
2
votes
3
replies
655
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by
meghanapple2
• 0 • written 11 months ago by
Chris
▴ 10
4
votes
4
replies
846
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
11 months ago • updated 10 months ago
bhandary.8590
▴ 20
50 results • Page
1 of 1
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ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
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Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
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Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
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Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
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Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
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Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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