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diffBind
•
reset
0
votes
0
replies
26
views
dba.plotProfile() plotting and interpretation
DiffBind
16 hours ago
Henry
▴ 10
0
votes
0
replies
34
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
1 day ago
yvonneh
• 0
0
votes
0
replies
27
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
1 day ago
Ian D.
▴ 70
0
votes
2
replies
105
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
2 days ago • updated 1 day ago
Ian D.
▴ 70
1
vote
1
reply
93
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
marcusn
• 0
0
votes
1
reply
123
views
ATACseq merge peaks
DiffBind
updated 7 days ago by
ATpoint
★ 4.1k • written 9 days ago by
Shloka
• 0
0
votes
4
replies
234
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
16 days ago • updated 14 days ago
lonn
• 0
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
18 days ago
Virangika
• 0
2
votes
2
replies
170
views
[DiffBind] Obtaining normalization factors
DiffBind
21 days ago • updated 18 days ago
Henry
▴ 10
2
votes
2
replies
384
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
22 days ago • updated 21 days ago
Henry
▴ 10
0
votes
0
replies
110
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
5 weeks ago
feather-W
• 0
0
votes
0
replies
109
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
5 weeks ago
Ankit
▴ 20
0
votes
0
replies
96
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
139
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
6 weeks ago
erbrocato
• 0
0
votes
2
replies
244
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago
Sam
▴ 10
0
votes
1
reply
197
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
299
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
244
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
176
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
168
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
0
votes
0
replies
238
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
4 months ago
Hai
• 0
0
votes
0
replies
257
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
1
vote
2
replies
326
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
0
votes
2
replies
352
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by
Sam
▴ 10
1
vote
1
reply
354
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 4 months ago by
ATpoint
★ 4.1k • written 5 months ago by
Miquel
• 0
0
votes
0
replies
332
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
408
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
2
replies
466
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago • updated 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 7 months ago by
r.murakami
• 0
1
vote
1
reply
449
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
0
votes
3
replies
632
views
diffbind analyze for wheat
DiffBind
updated 9 weeks ago by
Igor
• 0 • written 7 months ago by
zgyu12
• 0
3
votes
7
replies
861
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 7 months ago by
Chris
• 0
0
votes
1
reply
543
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
933
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
484
views
DiffBind error
DiffBind
updated 8 months ago by
Rory Stark
★ 5.2k • written 8 months ago by
M.Vukic
• 0
1
vote
2
replies
624
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago
Junsik
• 0
0
votes
3
replies
631
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
2
replies
836
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
3.0k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • 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
★ 5.2k • written 9 months ago by
bhandary.8590
▴ 20
1
vote
4
replies
871
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago
Theo
▴ 10
1
vote
2
replies
681
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
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
2
votes
3
replies
615
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
816
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
1
vote
2
replies
777
views
Interpret plots from DiffBind
DiffBind
10 months ago
Chris
• 0
0
votes
1
reply
545
views
DiffBind output issues
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
David.Atkinson2
• 0
0
votes
0
replies
429
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
0
votes
0
replies
411
views
Title in dba.plotProfile
DiffBind
11 months ago
agata17
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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