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diffbind
•
reset
0
votes
5
replies
58
views
Diffbind interpretation of data - fold change
DiffBind
4 hours ago • updated 2 hours ago
Vera
• 0
0
votes
0
replies
181
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
9 weeks ago
kim
• 0
0
votes
0
replies
145
views
diffbind covariates
DiffBind
ATACSeq
updated 10 weeks ago by
Michael Love
43k • written 10 weeks ago by
Alpesh Querer
▴ 220
0
votes
2
replies
499
views
DiffBind dba.report discrepancy
DiffBind
11 weeks ago • updated 10 weeks ago
aelbassiouny
• 0
0
votes
0
replies
108
views
DiffBind subset replicates
DiffBind
12 weeks ago
Haiping
• 0
0
votes
0
replies
189
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
3 months ago
Young Boqin
• 0
0
votes
0
replies
234
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
3 months ago
Alejandro
• 0
0
votes
2
replies
376
views
DiffBind for MBD-seq
MBD-seq
DiffBind
4 months ago
Marianna
▴ 20
0
votes
0
replies
263
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
4 months ago
Ian D.
▴ 70
0
votes
1
reply
303
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
4 months ago
mdidish
▴ 10
0
votes
0
replies
253
views
DiffBind dba.plotprofile y-axis range
DiffBind
4 months ago
Tara
• 0
0
votes
8
replies
761
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 5 months ago by
Rory Stark
★ 5.2k • written 5 months ago by
Marianna
▴ 20
1
vote
3
replies
499
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 5 months ago by
Rory Stark
★ 5.2k • written 5 months ago by
jesswhitts
• 0
0
votes
0
replies
394
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
6 months ago
gamma.jian
▴ 10
0
votes
2
replies
481
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
6 months ago
Mallory
• 0
0
votes
0
replies
270
views
Difference in Contrast in DiffBind
DiffBind
7 months ago
user_bioinfo
• 0
0
votes
0
replies
300
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
8 months ago
Dinesh
• 0
0
votes
1
reply
589
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 8 weeks ago by
B.N
• 0 • written 8 months ago by
Henry
▴ 10
0
votes
0
replies
387
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
8 months ago
yvonneh
• 0
0
votes
0
replies
295
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 months ago
Ian D.
▴ 70
0
votes
9
replies
1.3k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 months ago • updated 11 weeks ago
Ian D.
▴ 70
3
votes
1
reply
513
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
marcusn
▴ 10
0
votes
1
reply
780
views
ATACseq merge peaks
DiffBind
updated 8 months ago by
ATpoint
★ 4.6k • written 8 months ago by
Shloka
• 0
0
votes
4
replies
578
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
8 months ago
lonn
• 0
0
votes
0
replies
295
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
8 months ago
Virangika
• 0
2
votes
2
replies
643
views
[DiffBind] Obtaining normalization factors
DiffBind
9 months ago • updated 8 months ago
Henry
▴ 10
2
votes
2
replies
1.0k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
9 months ago
Henry
▴ 10
0
votes
0
replies
390
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
9 months ago
feather-W
• 0
0
votes
0
replies
396
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
9 months ago
Ankit
▴ 20
0
votes
0
replies
357
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
9 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
388
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
9 months ago
erbrocato
• 0
0
votes
2
replies
633
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
10 months ago • updated 9 months ago
Sam
▴ 10
0
votes
1
reply
481
views
Exact same results in Diffbind with different normalization methods
DiffBind
10 months ago • updated 9 months ago
red_bricks
▴ 60
0
votes
1
reply
633
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
11 months ago
isaromero8888
• 0
0
votes
0
replies
644
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
11 months ago
Jawahar
• 0
0
votes
0
replies
382
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
11 months ago
frueher
• 0
0
votes
0
replies
354
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
12 months ago
Aswathy
• 0
0
votes
0
replies
521
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
12 months ago
Hai
• 0
0
votes
0
replies
465
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
12 months ago
inna.gur
• 0
0
votes
1
reply
1.3k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 12 months ago by
qq809825706
• 0 • written 16 months ago by
Mark
• 0
0
votes
2
replies
648
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 13 months ago by
Sam
▴ 10
1
vote
2
replies
569
views
Inconsistent results in DiffBind
DiffBind
13 months ago
Sam
▴ 10
1
vote
1
reply
615
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 13 months ago by
ATpoint
★ 4.6k • written 13 months ago by
Miquel
• 0
0
votes
0
replies
655
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
13 months ago
jared.andrews07
▴ 30
0
votes
0
replies
662
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 15 months ago by
James W. MacDonald
67k • written 15 months ago by
sophie.hfliu
• 0
2
votes
4
replies
1.6k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 15 months ago by
Matt Eldridge
▴ 10 • written 15 months ago by
r.murakami
• 0
2
votes
2
replies
685
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
15 months ago
r.murakami
• 0
1
vote
1
reply
793
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 15 months ago by
James W. MacDonald
67k • written 15 months ago by
lin.pei26
• 0
3
votes
7
replies
1.4k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 16 months ago by
Chris
▴ 20
0
votes
3
replies
914
views
diffbind analyze for wheat
DiffBind
updated 10 months ago by
Igor
• 0 • written 16 months ago by
zgyu12
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Newbie Question - adding metadata to an analysis
by
Bryan H
• 0
Thanks for the documentation. I have most of it working, except for the most critical step - incorporating the new metadata with the datase…
Comment: Diffbind interpretation of data - fold change
by
Vera
• 0
Thank you for confirming that the foldchange is log2
Comment: Diffbind interpretation of data - fold change
by
Vera
• 0
This solved it!
Comment: Diffbind interpretation of data - fold change
by
Vera
• 0
Perfect! Thank you so much!
Answer: Diffbind interpretation of data - fold change
by
Rory Stark
★ 5.2k
For Question #2, note that by default, `dba.report()` only returns "differentially bound" intervals where the FDR is less than a threshold …
Votes
Answer: Package `not available for Bioconductor version '3.20'` when it should be
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: Theoretical WGCNA Question
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a
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