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Showing :
DiFFBind
•
reset
0
votes
0
replies
126
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
28 days ago
kim
• 0
0
votes
0
replies
109
views
diffbind covariates
DiffBind
ATACSeq
updated 5 weeks ago by
Michael Love
43k • written 5 weeks ago by
Alpesh Querer
▴ 220
0
votes
2
replies
444
views
DiffBind dba.report discrepancy
DiffBind
6 weeks ago • updated 5 weeks ago
aelbassiouny
• 0
0
votes
0
replies
88
views
DiffBind subset replicates
DiffBind
7 weeks ago
Haiping
• 0
0
votes
0
replies
143
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
7 weeks ago
Young Boqin
• 0
0
votes
0
replies
207
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
11 weeks ago
Alejandro
• 0
0
votes
2
replies
343
views
DiffBind for MBD-seq
MBD-seq
DiffBind
3 months ago
Marianna
▴ 20
0
votes
0
replies
232
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
3 months ago
Ian D.
▴ 70
0
votes
1
reply
273
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
3 months ago
mdidish
▴ 10
0
votes
0
replies
223
views
DiffBind dba.plotprofile y-axis range
DiffBind
3 months ago
Tara
• 0
0
votes
8
replies
718
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 3 months ago by
Rory Stark
★ 5.2k • written 4 months ago by
Marianna
▴ 20
1
vote
3
replies
468
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 4 months ago by
Rory Stark
★ 5.2k • written 4 months ago by
jesswhitts
• 0
0
votes
0
replies
350
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
5 months ago
gamma.jian
▴ 10
0
votes
2
replies
432
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
5 months ago
Mallory
• 0
0
votes
0
replies
246
views
Difference in Contrast in DiffBind
DiffBind
6 months ago
user_bioinfo
• 0
0
votes
0
replies
280
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
7 months ago
Dinesh
• 0
0
votes
1
reply
530
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 27 days ago by
B.N
• 0 • written 7 months ago by
Henry
▴ 10
0
votes
0
replies
353
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
7 months ago
yvonneh
• 0
0
votes
0
replies
276
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
1.2k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
7 months ago • updated 6 weeks ago
Ian D.
▴ 70
1
vote
1
reply
435
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
• 0
0
votes
1
reply
695
views
ATACseq merge peaks
DiffBind
updated 7 months ago by
ATpoint
★ 4.6k • written 7 months ago by
Shloka
• 0
0
votes
4
replies
545
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 months ago
lonn
• 0
0
votes
0
replies
267
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
7 months ago
Virangika
• 0
2
votes
2
replies
584
views
[DiffBind] Obtaining normalization factors
DiffBind
7 months ago
Henry
▴ 10
2
votes
2
replies
924
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
7 months ago
Henry
▴ 10
0
votes
0
replies
369
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
8 months ago
feather-W
• 0
0
votes
0
replies
361
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
8 months ago
Ankit
▴ 20
0
votes
0
replies
329
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
8 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
359
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 months ago
erbrocato
• 0
0
votes
2
replies
596
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 months ago
Sam
▴ 10
0
votes
1
reply
448
views
Exact same results in Diffbind with different normalization methods
DiffBind
8 months ago
red_bricks
▴ 60
0
votes
1
reply
589
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
10 months ago
isaromero8888
• 0
0
votes
0
replies
597
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
10 months ago
Jawahar
• 0
0
votes
0
replies
357
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
10 months ago
frueher
• 0
0
votes
0
replies
327
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
10 months ago
Aswathy
• 0
0
votes
0
replies
491
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
11 months ago
Hai
• 0
0
votes
0
replies
441
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
11 months ago
inna.gur
• 0
0
votes
1
reply
1.2k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 11 months ago by
qq809825706
• 0 • written 15 months ago by
Mark
• 0
0
votes
2
replies
611
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 12 months ago by
Sam
▴ 10
1
vote
2
replies
541
views
Inconsistent results in DiffBind
DiffBind
11 months ago
Sam
▴ 10
1
vote
1
reply
589
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
624
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
12 months ago
jared.andrews07
▴ 30
0
votes
0
replies
629
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
1.5k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 13 months ago by
Matt Eldridge
▴ 10 • written 14 months ago by
r.murakami
• 0
2
votes
2
replies
664
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
14 months ago
r.murakami
• 0
1
vote
1
reply
761
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 14 months ago by
James W. MacDonald
67k • written 14 months ago by
lin.pei26
• 0
3
votes
7
replies
1.3k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 14 months ago by
Chris
▴ 20
0
votes
3
replies
893
views
diffbind analyze for wheat
DiffBind
updated 9 months ago by
Igor
• 0 • written 14 months ago by
zgyu12
• 0
0
votes
1
reply
821
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
15 months ago
Mark
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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mikat
• 0
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joseph.joonsang
• 0
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Hans-Ulrich Klein
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shepherl
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