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diffbind
•
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0
votes
0
replies
18
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
6 hours ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
79
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
7 days ago
erbrocato
• 0
0
votes
1
reply
143
views
Exact same results in Diffbind with different normalization methods
DiffBind
16 days ago • updated 11 days ago
red_bricks
▴ 50
0
votes
2
replies
173
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
16 days ago • updated 14 days ago
Sam
▴ 10
0
votes
3
replies
1.1k
views
Blacklist error in DiffBind
DiffBind
Blacklist
updated 19 days ago by
marram_wang
• 0 • written 16 months ago by
Romain
• 0
0
votes
3
replies
554
views
diffbind analyze for wheat
DiffBind
updated 28 days ago by
Igor
• 0 • written 6 months ago by
zgyu12
• 0
2
votes
4
replies
1.2k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 5 weeks ago by
marcusn
• 0 • written 2.3 years ago by
bhanu.chandra1
• 0
0
votes
4
replies
1.9k
views
Subtracting INPUT reads from ChIP read counts.
diffbind
ChIP-seq
updated 9 weeks ago by
Rory Stark
★ 5.1k • written 7.7 years ago by
xie186
• 0
1
vote
7
replies
2.8k
views
Technical details of DiffBind correlation analysis
diffbind
duplicatecorrelation
updated 9 weeks ago by
Rory Stark
★ 5.1k • written 9.4 years ago by
meisan406
• 0
0
votes
1
reply
240
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
9 weeks ago
isaromero8888
• 0
0
votes
0
replies
164
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
9 weeks ago
Jawahar
• 0
0
votes
0
replies
125
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
10 weeks ago
frueher
• 0
1
vote
4
replies
939
views
Diffbind error while running example data
DiffBind
written 3.1 years ago by
Lucky
• 0
0
votes
0
replies
130
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
10 weeks ago
Aswathy
• 0
2
votes
3
replies
560
views
Sample sheet file for DiffBind
DiffBind
updated 11 weeks ago by
meghanapple2
• 0 • written 9 months ago by
Chris
• 0
0
votes
0
replies
181
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
12 weeks ago
Hai
• 0
0
votes
0
replies
203
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
3 months ago
inna.gur
• 0
0
votes
1
reply
878
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
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 3 months ago by
Rory Stark
★ 5.1k • written 6.5 years ago by
kyliecode
• 0
1
vote
2
replies
274
views
Inconsistent results in DiffBind
DiffBind
3 months ago
Sam
▴ 10
0
votes
2
replies
297
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 3 months ago by
Sam
▴ 10
1
vote
1
reply
290
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
Miquel
• 0
1
vote
7
replies
1.1k
views
Diffbind "No genome detected"
DiffBind
updated 4 months ago by
James W. MacDonald
65k • written 9 months ago by
kyliecode
• 0
0
votes
0
replies
282
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
4 months ago
jared.andrews07
▴ 30
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 5 months ago by
Matt Eldridge
• 0 • written 5 months ago by
r.murakami
• 0
2
votes
2
replies
423
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
5 months ago
r.murakami
• 0
0
votes
0
replies
342
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
sophie.hfliu
• 0
0
votes
5
replies
1.0k
views
DiffBind handling of replicates and consensus
diffbind
updated 6 months ago by
Rory Stark
★ 5.1k • written 4.1 years ago by
Jim
• 0
1
vote
1
reply
391
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
792
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 6 months ago by
Chris
• 0
0
votes
1
reply
494
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
556
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
7 months ago
Junsik
• 0
0
votes
2
replies
418
views
DiffBind error
DiffBind
updated 7 months ago by
Rory Stark
★ 5.1k • written 7 months ago by
M.Vukic
• 0
5
votes
19
replies
5.7k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 7 months ago by
liz.lamarca
• 0 • written 2.7 years ago by
kwangbom
▴ 10
0
votes
2
replies
740
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
1.7k
views
Help with error DiffBind
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
Chris
• 0
2
votes
3
replies
1.1k
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 3.0 years ago by
Sam
▴ 10
1
vote
1
reply
2.0k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
bhandary.8590
▴ 20
0
votes
5
replies
2.7k
views
diffbind
DiffBind
chipseq
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
ANAMIKA
• 0
0
votes
3
replies
547
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
4
replies
752
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
8 months ago
Theo
• 0
1
vote
2
replies
622
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
Stevie Pederson
• 0
4
votes
4
replies
743
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
9 months ago
bhandary.8590
▴ 20
0
votes
1
reply
506
views
DiffBind output issues
DiffBind
updated 9 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
David.Atkinson2
• 0
1
vote
2
replies
702
views
Interpret plots from DiffBind
DiffBind
9 months ago
Chris
• 0
7
votes
13
replies
1.7k
views
Interpret plot from DiffBind
DiffBind
updated 9 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
Chris
• 0
0
votes
5
replies
1.3k
views
DiffBind:all samples have 0 counts for all genes.
DiffBind
Genrich
updated 9 months ago by
xm00262
• 0 • written 3.4 years ago by
peris_baba
• 0
0
votes
0
replies
382
views
Help with error running DiffBind
DiffBind
9 months ago
Chris
• 0
1
vote
4
replies
921
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
2
votes
3
replies
728
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 10 months ago by
jandrade
• 0
50 results • Page
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Answer: WGCNA: analysis of complex trait associations with regressions
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
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mercedeh.movassagh
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Yes that is correct
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Gordon Smyth
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It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
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It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
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Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
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