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Diffbind
•
reset
0
votes
3
replies
199
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
9 days ago • updated 2 days ago
Ian D.
▴ 70
0
votes
0
replies
49
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
4 days ago
Dinesh
• 0
0
votes
0
replies
91
views
dba.plotProfile() plotting and interpretation
DiffBind
7 days ago
Henry
▴ 10
0
votes
0
replies
66
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
8 days ago
yvonneh
• 0
0
votes
0
replies
62
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 days ago
Ian D.
▴ 70
1
vote
1
reply
134
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 10 days ago by
Michael Love
42k • written 10 days ago by
marcusn
• 0
0
votes
1
reply
146
views
ATACseq merge peaks
DiffBind
updated 14 days ago by
ATpoint
★ 4.1k • written 16 days ago by
Shloka
• 0
0
votes
4
replies
246
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
23 days ago • updated 20 days ago
lonn
• 0
2
votes
2
replies
175
views
[DiffBind] Obtaining normalization factors
DiffBind
28 days ago • updated 24 days ago
Henry
▴ 10
0
votes
0
replies
100
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
25 days ago
Virangika
• 0
2
votes
2
replies
395
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
29 days ago • updated 28 days ago
Henry
▴ 10
0
votes
0
replies
117
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
6 weeks ago
feather-W
• 0
0
votes
0
replies
115
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
6 weeks ago
Ankit
▴ 20
0
votes
0
replies
102
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
6 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
145
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
7 weeks ago
erbrocato
• 0
0
votes
1
reply
203
views
Exact same results in Diffbind with different normalization methods
DiffBind
8 weeks ago • updated 7 weeks ago
red_bricks
▴ 50
0
votes
2
replies
258
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 weeks ago
Sam
▴ 10
0
votes
3
replies
1.1k
views
Blacklist error in DiffBind
DiffBind
Blacklist
updated 8 weeks ago by
marram_wang
• 0 • written 18 months ago by
Romain
• 0
0
votes
3
replies
643
views
diffbind analyze for wheat
DiffBind
updated 10 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 12 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 7.9 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
310
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
254
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
181
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
1
vote
4
replies
1.0k
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by
Lucky
• 0
0
votes
0
replies
176
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
2
votes
3
replies
633
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by
meghanapple2
• 0 • written 10 months ago by
Chris
• 0
0
votes
0
replies
250
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
4 months ago
Hai
• 0
0
votes
0
replies
266
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
0
votes
1
reply
946
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
1.9k
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
334
views
Inconsistent results in DiffBind
DiffBind
5 months ago • updated 4 months ago
Sam
▴ 10
0
votes
2
replies
365
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by
Sam
▴ 10
1
vote
1
reply
364
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 5 months ago by
ATpoint
★ 4.1k • written 5 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
338
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 7 months ago by
Matt Eldridge
• 0 • written 7 months ago by
r.murakami
• 0
2
votes
2
replies
470
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago
r.murakami
• 0
0
votes
0
replies
414
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
1.2k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by
Rory Stark
★ 5.2k • written 4.3 years ago by
Jim
• 0
1
vote
1
reply
462
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
875
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 8 months ago by
Chris
• 0
0
votes
1
reply
554
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
641
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago
Junsik
• 0
0
votes
2
replies
494
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
853
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
2.0k
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
50 results • Page
1 of 1
Recent ...
Replies
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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