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Showing :
diffBind
•
reset
0
votes
0
replies
162
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
7 weeks ago
kim
• 0
0
votes
0
replies
134
views
diffbind covariates
DiffBind
ATACSeq
updated 8 weeks ago by
Michael Love
43k • written 8 weeks ago by
Alpesh Querer
▴ 220
0
votes
2
replies
480
views
DiffBind dba.report discrepancy
DiffBind
9 weeks ago
aelbassiouny
• 0
0
votes
0
replies
103
views
DiffBind subset replicates
DiffBind
10 weeks ago
Haiping
• 0
0
votes
0
replies
176
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
11 weeks ago
Young Boqin
• 0
0
votes
0
replies
227
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
3 months ago
Alejandro
• 0
0
votes
2
replies
365
views
DiffBind for MBD-seq
MBD-seq
DiffBind
4 months ago • updated 3 months ago
Marianna
▴ 20
0
votes
0
replies
257
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
4 months ago
Ian D.
▴ 70
0
votes
1
reply
293
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
4 months ago
mdidish
▴ 10
0
votes
0
replies
245
views
DiffBind dba.plotprofile y-axis range
DiffBind
4 months ago
Tara
• 0
0
votes
8
replies
745
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 4 months ago by
Rory Stark
★ 5.2k • written 4 months ago by
Marianna
▴ 20
1
vote
3
replies
491
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 5 months ago by
Rory Stark
★ 5.2k • written 5 months ago by
jesswhitts
• 0
0
votes
0
replies
384
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
6 months ago
gamma.jian
▴ 10
0
votes
2
replies
467
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
6 months ago
Mallory
• 0
0
votes
0
replies
265
views
Difference in Contrast in DiffBind
DiffBind
7 months ago
user_bioinfo
• 0
0
votes
0
replies
297
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
7 months ago
Dinesh
• 0
0
votes
1
reply
572
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 7 weeks ago by
B.N
• 0 • written 7 months ago by
Henry
▴ 10
0
votes
0
replies
375
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
7 months ago
yvonneh
• 0
0
votes
0
replies
292
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
7 months ago
Ian D.
▴ 70
0
votes
9
replies
1.3k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
7 months ago • updated 9 weeks ago
Ian D.
▴ 70
3
votes
1
reply
501
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
marcusn
▴ 10
0
votes
1
reply
748
views
ATACseq merge peaks
DiffBind
updated 8 months ago by
ATpoint
★ 4.6k • written 8 months ago by
Shloka
• 0
0
votes
4
replies
569
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
8 months ago
lonn
• 0
0
votes
0
replies
285
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
8 months ago
Virangika
• 0
2
votes
2
replies
622
views
[DiffBind] Obtaining normalization factors
DiffBind
8 months ago
Henry
▴ 10
2
votes
2
replies
999
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
8 months ago
Henry
▴ 10
0
votes
0
replies
379
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
9 months ago
feather-W
• 0
0
votes
0
replies
385
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
9 months ago
Ankit
▴ 20
0
votes
0
replies
350
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
9 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
378
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
9 months ago
erbrocato
• 0
0
votes
2
replies
623
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 months ago
Sam
▴ 10
0
votes
1
reply
475
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 months ago
red_bricks
▴ 60
0
votes
1
reply
624
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
11 months ago
isaromero8888
• 0
0
votes
0
replies
630
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
11 months ago
Jawahar
• 0
0
votes
0
replies
373
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
11 months ago
frueher
• 0
0
votes
0
replies
346
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
11 months ago
Aswathy
• 0
0
votes
0
replies
513
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
11 months ago
Hai
• 0
0
votes
0
replies
459
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
12 months ago
inna.gur
• 0
0
votes
1
reply
1.2k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 12 months ago by
qq809825706
• 0 • written 16 months ago by
Mark
• 0
0
votes
2
replies
641
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 12 months ago by
Sam
▴ 10
1
vote
2
replies
559
views
Inconsistent results in DiffBind
DiffBind
12 months ago
Sam
▴ 10
1
vote
1
reply
605
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 12 months ago by
ATpoint
★ 4.6k • written 12 months ago by
Miquel
• 0
0
votes
0
replies
643
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
13 months ago
jared.andrews07
▴ 30
0
votes
0
replies
651
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 14 months ago by
James W. MacDonald
67k • written 14 months ago by
sophie.hfliu
• 0
2
votes
4
replies
1.6k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 14 months ago by
Matt Eldridge
▴ 10 • written 14 months ago by
r.murakami
• 0
2
votes
2
replies
678
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
14 months ago
r.murakami
• 0
1
vote
1
reply
783
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 15 months ago by
James W. MacDonald
67k • written 15 months ago by
lin.pei26
• 0
3
votes
7
replies
1.3k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 15 months ago by
Chris
▴ 20
0
votes
3
replies
906
views
diffbind analyze for wheat
DiffBind
updated 10 months ago by
Igor
• 0 • written 15 months ago by
zgyu12
• 0
0
votes
1
reply
844
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
16 months ago
Mark
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
by
O'Brien
• 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts
by
O'Brien
• 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Comment: Packages don't update, but no error or warning is thrown
by
neighsanlo
• 0
This is useful information.
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
freemanmclaughlin9969289
• 0
Tools such as Pathway Analysis with Deweighting of Overlapping Genes ([block blast][1]) or Gene Set Enrichment Analysis for Single Cell RNA…
Comment: How to get around the warning message: mzR has been built against a different Rc
by
Nan
• 0
Hello, I was wondering if you were able to resolve this issue? I've recently encountered a similar problem and would like to ask for your a…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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