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DiffBind
•
reset
0
votes
4
replies
188
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
6 days ago • updated 4 days ago
lonn
• 0
0
votes
0
replies
76
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
8 days ago
Virangika
• 0
2
votes
2
replies
143
views
[DiffBind] Obtaining normalization factors
DiffBind
11 days ago • updated 7 days ago
Henry
▴ 10
2
votes
2
replies
349
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
12 days ago • updated 11 days ago
Henry
▴ 10
0
votes
0
replies
96
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
25 days ago
feather-W
• 0
0
votes
0
replies
95
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
25 days ago
Ankit
▴ 20
0
votes
0
replies
83
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
26 days ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
125
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
4 weeks ago
erbrocato
• 0
0
votes
2
replies
227
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago • updated 5 weeks ago
Sam
▴ 10
0
votes
1
reply
185
views
Exact same results in Diffbind with different normalization methods
DiffBind
6 weeks ago • updated 5 weeks ago
red_bricks
▴ 50
0
votes
1
reply
285
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
227
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
164
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
155
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
0
votes
0
replies
221
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
3 months ago
Hai
• 0
0
votes
0
replies
239
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
3 months ago
inna.gur
• 0
1
vote
2
replies
317
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
0
votes
2
replies
332
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by
Sam
▴ 10
1
vote
1
reply
338
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
319
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
387
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
2
replies
453
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago
r.murakami
• 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
1
vote
1
reply
432
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
0
votes
3
replies
612
views
diffbind analyze for wheat
DiffBind
updated 7 weeks ago by
Igor
• 0 • written 7 months ago by
zgyu12
• 0
3
votes
7
replies
838
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 7 months ago by
Chris
• 0
0
votes
1
reply
531
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago
Mark
• 0
0
votes
1
reply
916
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by
qq809825706
• 0 • written 8 months ago by
Mark
• 0
0
votes
2
replies
453
views
DiffBind error
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
M.Vukic
• 0
1
vote
2
replies
595
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago
Junsik
• 0
0
votes
3
replies
605
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 9 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
jason.kost
• 0
0
votes
2
replies
794
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
0
votes
5
replies
2.9k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
ANAMIKA
• 0
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
bhandary.8590
▴ 20
1
vote
4
replies
829
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago
Theo
▴ 10
1
vote
2
replies
663
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
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
Chris
• 0
2
votes
3
replies
598
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
790
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
1
vote
2
replies
749
views
Interpret plots from DiffBind
DiffBind
10 months ago
Chris
• 0
0
votes
1
reply
534
views
DiffBind output issues
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
David.Atkinson2
• 0
0
votes
0
replies
417
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
0
votes
0
replies
400
views
Title in dba.plotProfile
DiffBind
10 months ago
agata17
• 0
7
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 11 months ago by
Chris
• 0
1
vote
4
replies
996
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 11 months ago by
lin.pei26
• 0
1
vote
0
replies
549
views
Fold values in Diffbind
DiffBind
11 months ago
bhandary.8590
▴ 20
0
votes
1
reply
646
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by
Rory Stark
★ 5.1k • written 11 months ago by
Shashank
• 0
2
votes
3
replies
773
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 11 months ago by
jandrade
• 0
0
votes
1
reply
551
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 11 months ago by
Rory Stark
★ 5.1k • written 11 months ago by
littlefishes20
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: get BM error
by
Fara
• 0
Thank you for the reply. The examples are these. ENSGACG00000014473 ENSGACG00000015168 ENSGACG00000007529
Comment: get BM error
by
Mike Smith
★ 6.5k
Can you provide an example of the Ensemble IDs you're trying to convert?
Comment: How to retrieve gene ontology GO class?
by
bandconductor
• 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
by
Michael Love
41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Votes
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
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