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Showing :
DiFFBind
•
reset
0
votes
0
replies
159
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
7 weeks ago
kim
• 0
0
votes
0
replies
131
views
diffbind covariates
DiffBind
ATACSeq
updated 8 weeks ago by
Michael Love
43k • written 8 weeks ago by
Alpesh Querer
▴ 220
0
votes
2
replies
475
views
DiffBind dba.report discrepancy
DiffBind
9 weeks ago • updated 8 weeks ago
aelbassiouny
• 0
0
votes
0
replies
99
views
DiffBind subset replicates
DiffBind
10 weeks ago
Haiping
• 0
0
votes
0
replies
172
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
10 weeks ago
Young Boqin
• 0
0
votes
0
replies
223
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
3 months ago
Alejandro
• 0
0
votes
2
replies
364
views
DiffBind for MBD-seq
MBD-seq
DiffBind
3 months ago
Marianna
▴ 20
0
votes
0
replies
251
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
288
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
4 months ago
mdidish
▴ 10
0
votes
0
replies
242
views
DiffBind dba.plotprofile y-axis range
DiffBind
4 months ago
Tara
• 0
0
votes
8
replies
741
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 4 months ago by
Rory Stark
★ 5.2k • written 4 months ago by
Marianna
▴ 20
1
vote
3
replies
489
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
378
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
6 months ago
gamma.jian
▴ 10
0
votes
2
replies
463
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
6 months ago
Mallory
• 0
0
votes
0
replies
261
views
Difference in Contrast in DiffBind
DiffBind
7 months ago
user_bioinfo
• 0
0
votes
0
replies
293
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
7 months ago
Dinesh
• 0
0
votes
1
reply
570
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 6 weeks ago by
B.N
• 0 • written 7 months ago by
Henry
▴ 10
0
votes
0
replies
374
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
7 months ago
yvonneh
• 0
0
votes
0
replies
288
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
7 months ago
Ian D.
▴ 70
0
votes
9
replies
1.3k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
7 months ago • updated 9 weeks ago
Ian D.
▴ 70
3
votes
1
reply
495
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 7 months ago by
Michael Love
43k • written 7 months ago by
marcusn
▴ 10
0
votes
1
reply
743
views
ATACseq merge peaks
DiffBind
updated 8 months ago by
ATpoint
★ 4.6k • written 8 months ago by
Shloka
• 0
0
votes
4
replies
567
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
282
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
8 months ago
Virangika
• 0
2
votes
2
replies
617
views
[DiffBind] Obtaining normalization factors
DiffBind
8 months ago
Henry
▴ 10
2
votes
2
replies
995
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
8 months ago
Henry
▴ 10
0
votes
0
replies
378
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
9 months ago
feather-W
• 0
0
votes
0
replies
381
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
9 months ago
Ankit
▴ 20
0
votes
0
replies
348
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
9 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
377
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
9 months ago
erbrocato
• 0
0
votes
2
replies
620
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 months ago
Sam
▴ 10
0
votes
1
reply
472
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 months ago
red_bricks
▴ 60
0
votes
1
reply
623
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
630
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
371
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
11 months ago
frueher
• 0
0
votes
0
replies
345
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
11 months ago
Aswathy
• 0
0
votes
0
replies
512
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
11 months ago
Hai
• 0
0
votes
0
replies
457
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
12 months ago
inna.gur
• 0
0
votes
1
reply
1.2k
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
638
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 12 months ago by
Sam
▴ 10
1
vote
2
replies
558
views
Inconsistent results in DiffBind
DiffBind
12 months ago
Sam
▴ 10
1
vote
1
reply
604
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 12 months ago by
ATpoint
★ 4.6k • written 12 months ago by
Miquel
• 0
0
votes
0
replies
642
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
650
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 14 months ago by
James W. MacDonald
67k • written 14 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 14 months ago by
Matt Eldridge
▴ 10 • written 14 months ago by
r.murakami
• 0
2
votes
2
replies
675
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
14 months ago
r.murakami
• 0
1
vote
1
reply
782
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
1.3k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 15 months ago by
Chris
▴ 20
0
votes
3
replies
905
views
diffbind analyze for wheat
DiffBind
updated 9 months ago by
Igor
• 0 • written 15 months ago by
zgyu12
• 0
0
votes
1
reply
844
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
16 months ago
Mark
• 0
50 results • Page
1 of 1
Recent ...
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Comment: How to get around the warning message: mzR has been built against a different Rc
by
Nan
• 0
Hello, I was wondering if you were able to resolve this issue? I've recently encountered a similar problem and would like to ask for your a…
Answer: EuroBioC2023 abstract submission closing soon!
by
excess.gecko.shso
• 0
Don't miss out! EuroBioC2023 abstract submissions are nearing the deadline. Sharpen your scientific [Wordle Game][1] skills and submit your…
Answer: EuroBioC2024 abstract submission is open!
by
excess.gecko.shso
• 0
EuroBioC2024 abstract submissions are now open! Join the Oxford conference from Sep 4-6. Submit your abstract by April 26 for short talks, …
Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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