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DiffBind
•
reset
0
votes
3
replies
187
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 days ago • updated 1 day ago
Ian D.
▴ 70
0
votes
0
replies
38
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
2 days ago
Dinesh
• 0
0
votes
0
replies
80
views
dba.plotProfile() plotting and interpretation
DiffBind
5 days ago
Henry
▴ 10
0
votes
0
replies
59
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
6 days ago
yvonneh
• 0
0
votes
0
replies
53
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
6 days ago
Ian D.
▴ 70
1
vote
1
reply
129
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 9 days ago by
Michael Love
42k • written 9 days ago by
marcusn
• 0
0
votes
1
reply
142
views
ATACseq merge peaks
DiffBind
updated 13 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Shloka
• 0
0
votes
4
replies
244
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
22 days ago • updated 19 days ago
lonn
• 0
2
votes
2
replies
173
views
[DiffBind] Obtaining normalization factors
DiffBind
26 days ago • updated 23 days ago
Henry
▴ 10
0
votes
0
replies
96
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
23 days ago
Virangika
• 0
2
votes
2
replies
394
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
27 days ago • updated 26 days ago
Henry
▴ 10
0
votes
0
replies
115
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
5 weeks ago
feather-W
• 0
0
votes
0
replies
114
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
5 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
144
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
256
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
640
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 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 7.9 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
307
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
252
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
179
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
173
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago
Aswathy
• 0
2
votes
3
replies
629
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
246
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
4 months ago
Hai
• 0
0
votes
0
replies
264
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
0
votes
1
reply
943
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
333
views
Inconsistent results in DiffBind
DiffBind
4 months ago
Sam
▴ 10
0
votes
2
replies
360
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by
Sam
▴ 10
1
vote
1
reply
361
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
337
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
412
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
460
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
870
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 7 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
637
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
493
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
851
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
50 results • Page
1 of 1
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Comment: DSS CpG coverage threshold
by
j.gilbert
• 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
Comment: deseq2 results
by
sajadahmad41454
• 0
could you please tell me if the results are fine or not? ![pca summary][1] ![pca plot][2] [1]: /media/images/ee7d8693-bcbe-4a7a-a566-d3…
Answer: normalization using Deseq2
by
ATpoint
★ 4.1k
counts(dds, normalized=TRUE)
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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