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DiffBind
•
reset
0
votes
0
replies
25
views
Difference in Contrast in DiffBind
DiffBind
1 day ago
zzrammal
• 0
0
votes
4
replies
358
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by
Ziliang
• 0 • written 15 days ago by
Ian D.
▴ 70
0
votes
0
replies
82
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
10 days ago
Dinesh
• 0
0
votes
0
replies
115
views
dba.plotProfile() plotting and interpretation
DiffBind
13 days ago
Henry
▴ 10
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
14 days ago
yvonneh
• 0
0
votes
0
replies
81
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
14 days ago
Ian D.
▴ 70
1
vote
1
reply
150
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 16 days ago by
Michael Love
42k • written 16 days ago by
marcusn
• 0
0
votes
1
reply
167
views
ATACseq merge peaks
DiffBind
updated 20 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Shloka
• 0
0
votes
4
replies
261
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
29 days ago • updated 26 days ago
lonn
• 0
2
votes
2
replies
189
views
[DiffBind] Obtaining normalization factors
DiffBind
4 weeks ago
Henry
▴ 10
0
votes
0
replies
105
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 weeks ago
Virangika
• 0
2
votes
2
replies
412
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
0
votes
0
replies
123
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
6 weeks ago
feather-W
• 0
0
votes
0
replies
120
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
6 weeks ago
Ankit
▴ 20
0
votes
0
replies
109
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
7 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
149
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 weeks ago
erbrocato
• 0
0
votes
1
reply
211
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago • updated 8 weeks ago
red_bricks
▴ 50
0
votes
2
replies
269
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago
Sam
▴ 10
0
votes
3
replies
1.2k
views
Blacklist error in DiffBind
DiffBind
Blacklist
updated 9 weeks ago by
marram_wang
• 0 • written 18 months ago by
Romain
• 0
0
votes
3
replies
655
views
diffbind analyze for wheat
DiffBind
updated 11 weeks ago by
Igor
• 0 • written 8 months ago by
zgyu12
• 0
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 3 months ago by
marcusn
• 0 • written 2.4 years ago by
bhanu.chandra1
• 0
0
votes
4
replies
2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind
ChIP-seq
updated 3 months ago by
Rory Stark
★ 5.2k • written 7.9 years ago by
xie186
• 0
1
vote
7
replies
3.0k
views
Technical details of DiffBind correlation analysis
diffbind
duplicatecorrelation
updated 3 months ago by
Rory Stark
★ 5.2k • written 9.5 years ago by
meisan406
• 0
0
votes
1
reply
323
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
265
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
187
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
1
vote
4
replies
1.0k
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by
Lucky
• 0
0
votes
0
replies
183
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
4 months ago
Aswathy
• 0
2
votes
3
replies
648
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by
meghanapple2
• 0 • written 11 months ago by
Chris
▴ 10
0
votes
0
replies
265
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
4 months ago
Hai
• 0
0
votes
0
replies
277
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
0
votes
1
reply
953
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
1
vote
3
replies
1.9k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 5 months ago by
Rory Stark
★ 5.2k • written 6.6 years ago by
kyliecode
• 0
1
vote
2
replies
346
views
Inconsistent results in DiffBind
DiffBind
5 months ago
Sam
▴ 10
0
votes
2
replies
374
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by
Sam
▴ 10
1
vote
1
reply
372
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
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
0
votes
0
replies
347
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
6 months ago
jared.andrews07
▴ 30
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
479
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago
r.murakami
• 0
0
votes
0
replies
425
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
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
1
reply
469
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
880
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 8 months ago by
Chris
▴ 10
0
votes
1
reply
565
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
654
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
503
views
DiffBind error
DiffBind
updated 8 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
M.Vukic
• 0
5
votes
19
replies
6.0k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
0
votes
2
replies
872
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
50 results • Page
1 of 1
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
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makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
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