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diffBind
•
reset
0
votes
0
replies
15
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
14 hours ago
lonn
• 0
0
votes
0
replies
45
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
2 days ago
Virangika
• 0
2
votes
2
replies
123
views
[DiffBind] Obtaining normalization factors
DiffBind
5 days ago • updated 1 day ago
Henry
▴ 10
2
votes
2
replies
331
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
6 days ago • updated 5 days ago
Henry
▴ 10
0
votes
0
replies
91
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
19 days ago
feather-W
• 0
0
votes
0
replies
85
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
19 days ago
Ankit
▴ 20
0
votes
0
replies
76
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
20 days ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
116
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
28 days ago
erbrocato
• 0
0
votes
2
replies
215
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
5 weeks ago • updated 4 weeks ago
Sam
▴ 10
0
votes
1
reply
174
views
Exact same results in Diffbind with different normalization methods
DiffBind
5 weeks ago • updated 4 weeks ago
red_bricks
▴ 50
0
votes
1
reply
276
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
12 weeks ago
isaromero8888
• 0
0
votes
0
replies
218
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
12 weeks ago
Jawahar
• 0
0
votes
0
replies
157
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
147
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
0
votes
0
replies
210
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
3 months ago
Hai
• 0
0
votes
0
replies
231
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
3 months ago
inna.gur
• 0
0
votes
1
reply
904
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by
qq809825706
• 0 • written 7 months ago by
Mark
• 0
0
votes
2
replies
321
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by
Sam
▴ 10
1
vote
2
replies
307
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
1
vote
1
reply
331
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
Miquel
• 0
0
votes
0
replies
311
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
5 months ago
jared.andrews07
▴ 30
0
votes
0
replies
379
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
sophie.hfliu
• 0
2
votes
4
replies
1.2k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 6 months ago by
Matt Eldridge
• 0 • written 6 months ago by
r.murakami
• 0
2
votes
2
replies
446
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago
r.murakami
• 0
1
vote
1
reply
423
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
lin.pei26
• 0
3
votes
7
replies
828
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 7 months ago by
Chris
• 0
0
votes
3
replies
597
views
diffbind analyze for wheat
DiffBind
updated 7 weeks ago by
Igor
• 0 • written 7 months ago by
zgyu12
• 0
0
votes
1
reply
520
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
7 months ago
Mark
• 0
1
vote
2
replies
585
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago • updated 7 months ago
Junsik
• 0
0
votes
2
replies
440
views
DiffBind error
DiffBind
updated 7 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
M.Vukic
• 0
0
votes
2
replies
782
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 8 months ago by
Malcolm Cook
★ 1.6k • written 8 months ago by
Nebat
• 0
1
vote
1
reply
1.8k
views
Help with error DiffBind
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
Chris
• 0
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 8 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
bhandary.8590
▴ 20
0
votes
5
replies
2.9k
views
diffbind
DiffBind
chipseq
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
ANAMIKA
• 0
0
votes
3
replies
596
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
jason.kost
• 0
0
votes
5
replies
1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 6 months ago by
Rory Stark
★ 5.1k • written 4.2 years ago by
Jim
• 0
1
vote
4
replies
808
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago
Theo
▴ 10
1
vote
2
replies
655
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
Stevie Pederson
• 0
0
votes
1
reply
527
views
DiffBind output issues
DiffBind
updated 9 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
David.Atkinson2
• 0
1
vote
2
replies
739
views
Interpret plots from DiffBind
DiffBind
10 months ago • updated 9 months ago
Chris
• 0
2
votes
3
replies
588
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by
meghanapple2
• 0 • written 10 months ago by
Chris
• 0
4
votes
4
replies
783
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago • updated 9 months ago
bhandary.8590
▴ 20
0
votes
0
replies
409
views
Help with error running DiffBind
DiffBind
10 months ago
Chris
• 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 4 months ago by
James W. MacDonald
65k • written 10 months ago by
kyliecode
• 0
7
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
Chris
• 0
0
votes
0
replies
391
views
Title in dba.plotProfile
DiffBind
10 months ago
agata17
• 0
0
votes
1
reply
545
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 10 months ago by
Rory Stark
★ 5.1k • written 11 months ago by
littlefishes20
▴ 10
0
votes
1
reply
635
views
DiffBind dba() in parallel
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
Shashank
• 0
1
vote
4
replies
980
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
lin.pei26
• 0
1
vote
0
replies
542
views
Fold values in Diffbind
DiffBind
10 months ago
bhandary.8590
▴ 20
50 results • Page
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Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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