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DiFFBind
•
reset
0
votes
0
replies
51
views
dba.plotProfile() plotting and interpretation
DiffBind
3 days ago
Henry
▴ 10
0
votes
0
replies
48
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
4 days ago
yvonneh
• 0
0
votes
0
replies
43
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
4 days ago
Ian D.
▴ 70
0
votes
2
replies
130
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
5 days ago • updated 4 days ago
Ian D.
▴ 70
1
vote
1
reply
108
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
marcusn
• 0
0
votes
1
reply
138
views
ATACseq merge peaks
DiffBind
updated 10 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Shloka
• 0
0
votes
4
replies
238
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
19 days ago • updated 16 days ago
lonn
• 0
0
votes
0
replies
95
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
21 days ago
Virangika
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
24 days ago • updated 20 days ago
Henry
▴ 10
2
votes
2
replies
390
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
25 days ago • updated 24 days ago
Henry
▴ 10
0
votes
0
replies
115
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
5 weeks ago
feather-W
• 0
0
votes
0
replies
111
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
5 weeks ago
Ankit
▴ 20
0
votes
0
replies
100
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
141
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
6 weeks ago
erbrocato
• 0
0
votes
2
replies
250
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago
Sam
▴ 10
0
votes
1
reply
200
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago
red_bricks
▴ 50
0
votes
1
reply
302
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
3 months ago
isaromero8888
• 0
0
votes
0
replies
246
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
3 months ago
Jawahar
• 0
0
votes
0
replies
177
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
170
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
0
votes
0
replies
243
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
4 months ago
Hai
• 0
0
votes
0
replies
261
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
0
votes
1
reply
940
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by
qq809825706
• 0 • written 8 months ago by
Mark
• 0
0
votes
2
replies
356
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by
Sam
▴ 10
1
vote
2
replies
331
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
1
vote
1
reply
358
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
Miquel
• 0
0
votes
0
replies
334
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
411
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 7 months ago by
James W. MacDonald
65k • written 7 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 7 months ago by
r.murakami
• 0
2
votes
2
replies
469
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago
r.murakami
• 0
1
vote
1
reply
454
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
lin.pei26
• 0
3
votes
7
replies
866
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 7 months ago by
Chris
• 0
0
votes
3
replies
636
views
diffbind analyze for wheat
DiffBind
updated 9 weeks ago by
Igor
• 0 • written 7 months ago by
zgyu12
• 0
0
votes
1
reply
547
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago
Mark
• 0
1
vote
2
replies
632
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago
Junsik
• 0
0
votes
2
replies
489
views
DiffBind error
DiffBind
updated 8 months ago by
Rory Stark
★ 5.2k • written 8 months ago by
M.Vukic
• 0
0
votes
2
replies
842
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 9 months ago by
Malcolm Cook
★ 1.6k • written 9 months ago by
Nebat
• 0
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
Chris
• 0
1
vote
1
reply
2.3k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
bhandary.8590
▴ 20
0
votes
5
replies
3.1k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
ANAMIKA
• 0
0
votes
3
replies
635
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
jason.kost
• 0
0
votes
5
replies
1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by
Rory Stark
★ 5.2k • written 4.2 years ago by
Jim
• 0
1
vote
4
replies
878
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago
Theo
▴ 10
1
vote
2
replies
688
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
Stevie Pederson
• 0
0
votes
1
reply
550
views
DiffBind output issues
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
David.Atkinson2
• 0
1
vote
2
replies
781
views
Interpret plots from DiffBind
DiffBind
10 months ago
Chris
• 0
2
votes
3
replies
618
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
823
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
0
votes
0
replies
432
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 5 months ago by
James W. MacDonald
65k • written 11 months ago by
kyliecode
• 0
50 results • Page
1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset)
by
Caio
• 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The left plot indicates you should use genome segmentation. It is what is called "nonstationary" meaning it looks like there are distinct r…
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
gene_bioconductor
▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
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