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diffbind
•
reset
0
votes
0
replies
12
views
dba.plotProfile() plotting and interpretation
DiffBind
2 hours ago
Henry
▴ 10
0
votes
0
replies
31
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
1 day ago
yvonneh
• 0
0
votes
0
replies
25
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
99
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
87
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
121
views
ATACseq merge peaks
DiffBind
updated 7 days ago by
ATpoint
★ 4.1k • written 9 days ago by
Shloka
• 0
0
votes
4
replies
233
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
16 days ago • updated 13 days ago
lonn
• 0
2
votes
2
replies
168
views
[DiffBind] Obtaining normalization factors
DiffBind
21 days ago • updated 17 days ago
Henry
▴ 10
0
votes
0
replies
93
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
18 days ago
Virangika
• 0
2
votes
2
replies
382
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
109
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
94
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
1
reply
195
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago
red_bricks
▴ 50
0
votes
2
replies
244
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago
Sam
▴ 10
0
votes
3
replies
1.1k
views
Blacklist error in DiffBind
DiffBind
Blacklist
updated 7 weeks ago by
marram_wang
• 0 • written 17 months ago by
Romain
• 0
0
votes
3
replies
631
views
diffbind analyze for wheat
DiffBind
updated 9 weeks ago by
Igor
• 0 • written 7 months ago by
zgyu12
• 0
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 11 weeks ago by
marcusn
• 0 • written 2.4 years ago by
bhanu.chandra1
• 0
0
votes
4
replies
2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind
ChIP-seq
updated 3 months ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
xie186
• 0
1
vote
7
replies
2.9k
views
Technical details of DiffBind correlation analysis
diffbind
duplicatecorrelation
updated 3 months ago by
Rory Stark
★ 5.2k • written 9.5 years ago by
meisan406
• 0
0
votes
1
reply
298
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
1
vote
4
replies
993
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by
Lucky
• 0
0
votes
0
replies
168
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
2
votes
3
replies
610
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by
meghanapple2
• 0 • written 10 months ago by
Chris
• 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
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
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 4 months ago by
Rory Stark
★ 5.2k • written 6.6 years ago by
kyliecode
• 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 4 months ago by
Miquel
• 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
332
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
5 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 6 months ago by
Matt Eldridge
• 0 • written 7 months ago by
r.murakami
• 0
2
votes
2
replies
465
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago • updated 6 months ago
r.murakami
• 0
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
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
1
reply
448
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
860
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
1
vote
2
replies
621
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago
Junsik
• 0
0
votes
2
replies
482
views
DiffBind error
DiffBind
updated 8 months ago by
Rory Stark
★ 5.2k • written 8 months ago by
M.Vukic
• 0
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
0
votes
2
replies
835
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
2
votes
3
replies
1.1k
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 9 months ago by
Rory Stark
★ 5.2k • written 3.1 years ago by
Sam
▴ 10
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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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