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diffbind
•
reset
0
votes
0
replies
20
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
12 hours ago
Ian D.
▴ 70
1
vote
1
reply
68
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
marcusn
• 0
0
votes
1
reply
107
views
ATACseq merge peaks
DiffBind
updated 5 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Shloka
• 0
0
votes
4
replies
219
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
14 days ago • updated 11 days ago
lonn
• 0
0
votes
0
replies
87
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
16 days ago
Virangika
• 0
2
votes
2
replies
163
views
[DiffBind] Obtaining normalization factors
DiffBind
19 days ago • updated 15 days ago
Henry
▴ 10
2
votes
2
replies
376
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
20 days ago • updated 19 days ago
Henry
▴ 10
0
votes
0
replies
106
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
4 weeks ago
feather-W
• 0
0
votes
0
replies
105
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
4 weeks ago
Ankit
▴ 20
0
votes
0
replies
92
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
4 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
136
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
6 weeks ago
erbrocato
• 0
0
votes
2
replies
239
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago • updated 6 weeks ago
Sam
▴ 10
0
votes
1
reply
193
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago
red_bricks
▴ 50
0
votes
1
reply
296
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
242
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
173
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
165
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
0
votes
0
replies
235
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
4 months ago
Hai
• 0
0
votes
0
replies
254
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
0
votes
1
reply
927
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
345
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by
Sam
▴ 10
1
vote
2
replies
324
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
1
vote
1
reply
352
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
Miquel
• 0
0
votes
0
replies
329
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
403
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 7 months ago by
r.murakami
• 0
2
votes
2
replies
461
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago
r.murakami
• 0
1
vote
1
reply
445
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
856
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 7 months ago by
Chris
• 0
0
votes
3
replies
628
views
diffbind analyze for wheat
DiffBind
updated 9 weeks ago by
Igor
• 0 • written 7 months ago by
zgyu12
• 0
0
votes
1
reply
541
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
614
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago
Junsik
• 0
0
votes
2
replies
477
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
825
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
2.2k
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
3.0k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
ANAMIKA
• 0
0
votes
3
replies
622
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
862
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago
Theo
▴ 10
1
vote
2
replies
674
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
Stevie Pederson
• 0
0
votes
1
reply
543
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
769
views
Interpret plots from DiffBind
DiffBind
10 months ago
Chris
• 0
2
votes
3
replies
606
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
806
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
0
votes
0
replies
425
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
8
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
Chris
• 0
0
votes
0
replies
408
views
Title in dba.plotProfile
DiffBind
11 months ago
agata17
• 0
0
votes
1
reply
559
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 11 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
littlefishes20
▴ 10
50 results • Page
1 of 1
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Replies
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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