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Showing :
DiFFBind
•
reset
0
votes
0
replies
75
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
3 days ago
kim
• 0
0
votes
0
replies
76
views
diffbind covariates
DiffBind
ATACSeq
updated 11 days ago by
Michael Love
42k • written 12 days ago by
Alpesh Querer
▴ 220
0
votes
2
replies
392
views
DiffBind dba.report discrepancy
DiffBind
20 days ago • updated 16 days ago
aelbassiouny
• 0
0
votes
0
replies
75
views
DiffBind subset replicates
DiffBind
24 days ago
Haiping
• 0
0
votes
0
replies
110
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
4 weeks ago
Young Boqin
• 0
0
votes
0
replies
185
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
7 weeks ago
Alejandro
• 0
0
votes
2
replies
322
views
DiffBind for MBD-seq
MBD-seq
DiffBind
10 weeks ago
Marianna
▴ 20
0
votes
0
replies
211
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
11 weeks ago
Ian D.
▴ 70
0
votes
1
reply
246
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
12 weeks ago
mdidish
▴ 10
0
votes
0
replies
203
views
DiffBind dba.plotprofile y-axis range
DiffBind
12 weeks ago
Tara
• 0
0
votes
8
replies
664
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 3 months ago by
Rory Stark
★ 5.2k • written 3 months ago by
Marianna
▴ 20
1
vote
3
replies
422
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 3 months ago by
Rory Stark
★ 5.2k • written 3 months ago by
jesswhitts
• 0
0
votes
0
replies
324
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
4 months ago
gamma.jian
▴ 10
0
votes
2
replies
396
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
4 months ago
Mallory
• 0
0
votes
0
replies
221
views
Difference in Contrast in DiffBind
DiffBind
5 months ago
user_bioinfo
• 0
0
votes
0
replies
265
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
6 months ago
Dinesh
• 0
0
votes
1
reply
483
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 2 days ago by
B.N
• 0 • written 6 months ago by
Henry
▴ 10
0
votes
0
replies
321
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
6 months ago
yvonneh
• 0
0
votes
0
replies
263
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
6 months ago
Ian D.
▴ 70
0
votes
9
replies
1.2k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
6 months ago • updated 21 days ago
Ian D.
▴ 70
1
vote
1
reply
409
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 6 months ago by
Michael Love
42k • written 6 months ago by
marcusn
• 0
0
votes
1
reply
647
views
ATACseq merge peaks
DiffBind
updated 6 months ago by
ATpoint
★ 4.5k • written 6 months ago by
Shloka
• 0
0
votes
4
replies
534
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
6 months ago
lonn
• 0
0
votes
0
replies
253
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
6 months ago
Virangika
• 0
2
votes
2
replies
538
views
[DiffBind] Obtaining normalization factors
DiffBind
7 months ago • updated 6 months ago
Henry
▴ 10
2
votes
2
replies
860
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
7 months ago
Henry
▴ 10
0
votes
0
replies
354
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
7 months ago
feather-W
• 0
0
votes
0
replies
346
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
7 months ago
Ankit
▴ 20
0
votes
0
replies
314
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
7 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
335
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
7 months ago
erbrocato
• 0
0
votes
2
replies
576
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 months ago • updated 7 months ago
Sam
▴ 10
0
votes
1
reply
423
views
Exact same results in Diffbind with different normalization methods
DiffBind
8 months ago • updated 7 months ago
red_bricks
▴ 60
0
votes
1
reply
558
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
9 months ago
isaromero8888
• 0
0
votes
0
replies
554
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
9 months ago
Jawahar
• 0
0
votes
0
replies
345
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
9 months ago
frueher
• 0
0
votes
0
replies
308
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
10 months ago
Aswathy
• 0
0
votes
0
replies
473
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
10 months ago
Hai
• 0
0
votes
0
replies
429
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
10 months ago
inna.gur
• 0
0
votes
1
reply
1.2k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 10 months ago by
qq809825706
• 0 • written 14 months ago by
Mark
• 0
0
votes
2
replies
592
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 11 months ago by
Sam
▴ 10
1
vote
2
replies
526
views
Inconsistent results in DiffBind
DiffBind
11 months ago
Sam
▴ 10
1
vote
1
reply
573
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 11 months ago by
ATpoint
★ 4.5k • written 11 months ago by
Miquel
• 0
0
votes
0
replies
605
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
11 months ago
jared.andrews07
▴ 30
0
votes
0
replies
612
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 13 months ago by
James W. MacDonald
67k • written 13 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 13 months ago by
r.murakami
• 0
2
votes
2
replies
642
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
13 months ago
r.murakami
• 0
1
vote
1
reply
736
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 13 months ago by
James W. MacDonald
67k • written 13 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
882
views
diffbind analyze for wheat
DiffBind
updated 8 months ago by
Igor
• 0 • written 14 months ago by
zgyu12
• 0
0
votes
1
reply
799
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
14 months ago
Mark
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet
by
Thili
• 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load
by
andrew.gibbons
• 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column
by
GV Yoshikawa
• 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet
by
Gordon Smyth
51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected.
by
Adam
• 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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Gordon Smyth
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to
Guido Hooiveld
★ 4.1k
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shepherl
4.1k
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Paul Harrison
▴ 100
Popular Question
to
Mikhail Dozmorov
▴ 30
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