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DiffBind
•
reset
0
votes
0
replies
24
views
DiffBind multi-tissue comparison
DiffBind
2 days ago
lryrainche
• 0
1
vote
2
replies
1.2k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
9 days ago • updated 8 days ago
Luca
• 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 14 days ago by
robert
• 0 • written 23 months ago by
Oscar
• 0
0
votes
0
replies
67
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
16 days ago
Harish
• 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 15 days ago by
Harry
• 0 • written 20 days ago by
tifaGis
• 0
0
votes
1
reply
140
views
building samplesheet and plot profile
DiffBind
7 weeks ago • updated 6 weeks ago
yf
• 0
0
votes
5
replies
372
views
Diffbind interpretation of data - fold change
DiffBind
10 weeks ago
Vera
• 0
0
votes
0
replies
295
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
4 months ago
kim
• 0
0
votes
0
replies
220
views
diffbind covariates
DiffBind
ATACSeq
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
658
views
DiffBind dba.report discrepancy
DiffBind
5 months ago • updated 4 months ago
aelbassiouny
• 0
0
votes
0
replies
156
views
DiffBind subset replicates
DiffBind
5 months ago
Haiping
• 0
0
votes
0
replies
305
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
5 months ago
Young Boqin
• 0
0
votes
0
replies
294
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
6 months ago
Alejandro
• 0
0
votes
2
replies
444
views
DiffBind for MBD-seq
MBD-seq
DiffBind
6 months ago
Marianna
▴ 20
0
votes
1
reply
504
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
7 months ago • updated 5 weeks ago
Ian D.
▴ 70
0
votes
1
reply
375
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
7 months ago
mdidish
▴ 10
0
votes
0
replies
314
views
DiffBind dba.plotprofile y-axis range
DiffBind
7 months ago
Tara
• 0
0
votes
8
replies
899
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 7 months ago by
Rory Stark
★ 5.2k • written 7 months ago by
Marianna
▴ 20
1
vote
3
replies
614
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 8 months ago by
Rory Stark
★ 5.2k • written 8 months ago by
jesswhitts
• 0
0
votes
0
replies
474
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
8 months ago
gamma.jian
▴ 10
0
votes
2
replies
600
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
9 months ago
Mallory
• 0
0
votes
0
replies
326
views
Difference in Contrast in DiffBind
DiffBind
10 months ago
user_bioinfo
• 0
0
votes
0
replies
354
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
10 months ago
Dinesh
• 0
0
votes
1
reply
700
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 4 months ago by
B.N
• 0 • written 10 months ago by
Henry
▴ 10
0
votes
0
replies
480
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
10 months ago
yvonneh
• 0
0
votes
0
replies
344
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
10 months ago
Ian D.
▴ 70
0
votes
9
replies
1.5k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
10 months ago • updated 5 months ago
Ian D.
▴ 70
3
votes
1
reply
661
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 10 months ago by
Michael Love
43k • written 10 months ago by
marcusn
▴ 10
0
votes
1
reply
966
views
ATACseq merge peaks
DiffBind
updated 10 months ago by
ATpoint
★ 4.7k • written 11 months ago by
Shloka
• 0
0
votes
4
replies
667
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
11 months ago
lonn
• 0
0
votes
0
replies
352
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
11 months ago
Virangika
• 0
2
votes
2
replies
765
views
[DiffBind] Obtaining normalization factors
DiffBind
11 months ago
Henry
▴ 10
2
votes
2
replies
1.2k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
11 months ago
Henry
▴ 10
0
votes
0
replies
453
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
11 months ago
feather-W
• 0
0
votes
0
replies
477
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
11 months ago
Ankit
▴ 20
0
votes
0
replies
424
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
11 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
441
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
12 months ago
erbrocato
• 0
0
votes
2
replies
715
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
12 months ago
Sam
▴ 10
0
votes
1
reply
538
views
Exact same results in Diffbind with different normalization methods
DiffBind
12 months ago
red_bricks
▴ 60
0
votes
1
reply
750
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
14 months ago
isaromero8888
• 0
0
votes
0
replies
735
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
14 months ago
Jawahar
• 0
0
votes
0
replies
434
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
14 months ago
frueher
• 0
0
votes
0
replies
418
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
14 months ago
Aswathy
• 0
0
votes
0
replies
586
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
14 months ago
Hai
• 0
0
votes
0
replies
517
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
14 months ago
inna.gur
• 0
0
votes
1
reply
1.4k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 14 months ago by
qq809825706
• 0 • written 19 months ago by
Mark
• 0
0
votes
2
replies
748
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 15 months ago by
Sam
▴ 10
1
vote
2
replies
631
views
Inconsistent results in DiffBind
DiffBind
15 months ago
Sam
▴ 10
1
vote
1
reply
682
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 15 months ago by
ATpoint
★ 4.7k • written 15 months ago by
Miquel
• 0
0
votes
0
replies
730
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
16 months ago
jared.andrews07
▴ 30
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESEQ2 looking at main effects while controlling for a continuous variable
by
James W. MacDonald
68k
The covariate is accounted for when you fit the model, so you don't need to do anything with it at the contrast step. You don't need a con…
Comment: DESEQ2 looking at main effects while controlling for a continuous variable
by
Lennie
• 0
Thank you so much for taking the time and for the detailed explanation! I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
by
James W. MacDonald
68k
If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…
Comment: Issue with DECIPHER::IdTaxa
by
Daniel
• 0
The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
by
Gordon Smyth
52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Votes
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
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• 0
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16k
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43k
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68k
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