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Showing :
DiFFBind
•
reset
0
votes
0
replies
84
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
4 days ago
Alejandro
• 0
0
votes
2
replies
264
views
DiffBind for MBD-seq
MBD-seq
DiffBind
23 days ago
Marianna
▴ 20
0
votes
0
replies
166
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
4 weeks ago
Ian D.
▴ 70
0
votes
1
reply
178
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
5 weeks ago
mdidish
▴ 10
0
votes
0
replies
159
views
DiffBind dba.plotprofile y-axis range
DiffBind
5 weeks ago
Tara
• 0
0
votes
8
replies
561
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 6 weeks ago by
Rory Stark
★ 5.2k • written 7 weeks ago by
Marianna
▴ 20
1
vote
3
replies
363
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 8 weeks ago by
Rory Stark
★ 5.2k • written 9 weeks ago by
jesswhitts
• 0
0
votes
0
replies
240
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
12 weeks ago
gamma.jian
• 0
0
votes
2
replies
324
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
3 months ago
Mallory
• 0
0
votes
0
replies
193
views
Difference in Contrast in DiffBind
DiffBind
4 months ago
user_bioinfo
• 0
0
votes
0
replies
235
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
4 months ago
Dinesh
• 0
0
votes
0
replies
293
views
dba.plotProfile() plotting and interpretation
DiffBind
4 months ago
Henry
▴ 10
0
votes
0
replies
256
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
4 months ago
yvonneh
• 0
0
votes
0
replies
225
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
4 months ago
Ian D.
▴ 70
0
votes
8
replies
942
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
4 months ago • updated 5 weeks ago
Ian D.
▴ 70
1
vote
1
reply
351
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 4 months ago by
Michael Love
42k • written 4 months ago by
marcusn
• 0
0
votes
1
reply
516
views
ATACseq merge peaks
DiffBind
updated 4 months ago by
ATpoint
★ 4.4k • written 4 months ago by
Shloka
• 0
0
votes
4
replies
464
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
5 months ago
lonn
• 0
0
votes
0
replies
211
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
5 months ago
Virangika
• 0
2
votes
2
replies
436
views
[DiffBind] Obtaining normalization factors
DiffBind
5 months ago
Henry
▴ 10
2
votes
2
replies
730
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 months ago
Henry
▴ 10
0
votes
0
replies
301
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
5 months ago
feather-W
• 0
0
votes
0
replies
305
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
5 months ago
Ankit
▴ 20
0
votes
0
replies
261
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
293
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
6 months ago
erbrocato
• 0
0
votes
2
replies
503
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 months ago
Sam
▴ 10
0
votes
1
reply
361
views
Exact same results in Diffbind with different normalization methods
DiffBind
6 months ago
red_bricks
▴ 60
0
votes
1
reply
496
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
8 months ago
isaromero8888
• 0
0
votes
0
replies
493
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
8 months ago
Jawahar
• 0
0
votes
0
replies
307
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
8 months ago
frueher
• 0
0
votes
0
replies
276
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
8 months ago
Aswathy
• 0
0
votes
0
replies
423
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
8 months ago
Hai
• 0
0
votes
0
replies
385
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
8 months ago
inna.gur
• 0
0
votes
1
reply
1.1k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 8 months ago by
qq809825706
• 0 • written 13 months ago by
Mark
• 0
0
votes
2
replies
528
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 9 months ago by
Sam
▴ 10
1
vote
2
replies
489
views
Inconsistent results in DiffBind
DiffBind
9 months ago
Sam
▴ 10
1
vote
1
reply
517
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 9 months ago by
ATpoint
★ 4.4k • written 9 months ago by
Miquel
• 0
0
votes
0
replies
545
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
10 months ago
jared.andrews07
▴ 30
0
votes
0
replies
566
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 11 months ago by
James W. MacDonald
67k • written 11 months ago by
sophie.hfliu
• 0
2
votes
4
replies
1.4k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 11 months ago by
Matt Eldridge
▴ 10 • written 11 months ago by
r.murakami
• 0
2
votes
2
replies
607
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
11 months ago
r.murakami
• 0
1
vote
1
reply
676
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 11 months ago by
James W. MacDonald
67k • written 11 months ago by
lin.pei26
• 0
3
votes
7
replies
1.2k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 12 months ago by
Chris
▴ 20
0
votes
3
replies
831
views
diffbind analyze for wheat
DiffBind
updated 6 months ago by
Igor
• 0 • written 12 months ago by
zgyu12
• 0
0
votes
5
replies
1.5k
views
DiffBind handling of replicates and consensus
diffbind
updated 11 months ago by
Rory Stark
★ 5.2k • written 4.6 years ago by
Jim
• 0
2
votes
3
replies
799
views
Sample sheet file for DiffBind
DiffBind
updated 8 months ago by
meghanapple2
• 0 • written 15 months ago by
Chris
▴ 20
1
vote
7
replies
1.6k
views
Diffbind "No genome detected"
DiffBind
updated 9 months ago by
James W. MacDonald
67k • written 15 months ago by
kyliecode
• 0
0
votes
3
replies
1.4k
views
Blacklist error in DiffBind
DiffBind
Blacklist
updated 6 months ago by
marram_wang
• 0 • written 22 months ago by
Romain
• 0
2
votes
4
replies
1.7k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 7 months ago by
marcusn
• 0 • written 2.8 years ago by
bhanu.chandra1
• 0
1
vote
4
replies
1.2k
views
Diffbind error while running example data
DiffBind
written 3.6 years ago by
Lucky
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Question on performing ANOVA-like analysis using limma
by
Gordon Smyth
51k
What does `sampleid` represent? If you use duplicateCorrelation(), then the blocking factor should be subject, it isn't clear from your que…
Answer: Question on performing ANOVA-like analysis using limma
by
Gordon Smyth
51k
In time course experiments such as this, it is essential to account for baseline variability between subjects, so the second analysis given…
Comment: AffylmGUI does not start wit R 4.4.1
by
Gordon Smyth
51k
Glad to hear that you have figured it out. Your experience might help other people with limmaGUI or affylmGUI on MacOS as well.
Answer: rtracklayer accessing UCSC data table not working
by
James W. MacDonald
67k
The track argument is deprecated now, so you can omit it. ``` > tbl.rmsk <- getTable(ucscTableQuery(mySession, table = "rmsk", range = …
Answer: For feline genome
by
James W. MacDonald
67k
This support site is meant to help people with specific questions about using Bioconductor software. There is a [vignette for `ROntoTools`]…
Votes
Comment: AffylmGUI does not start wit R 4.4.1
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Comment: Error in GOmeth function of missMethyl when EPICv2 annotation is used
Answer: unable to access Annotationhub latest record
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