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Showing :
Diffbind
•
reset
0
votes
0
replies
142
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
5 weeks ago
kim
• 0
0
votes
0
replies
119
views
diffbind covariates
DiffBind
ATACSeq
updated 6 weeks ago by
Michael Love
43k • written 6 weeks ago by
Alpesh Querer
▴ 220
0
votes
2
replies
457
views
DiffBind dba.report discrepancy
DiffBind
7 weeks ago
aelbassiouny
• 0
0
votes
0
replies
94
views
DiffBind subset replicates
DiffBind
8 weeks ago
Haiping
• 0
0
votes
0
replies
156
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
9 weeks ago
Young Boqin
• 0
0
votes
0
replies
214
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
12 weeks ago
Alejandro
• 0
0
votes
2
replies
352
views
DiffBind for MBD-seq
MBD-seq
DiffBind
3 months ago
Marianna
▴ 20
0
votes
0
replies
240
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
3 months ago
Ian D.
▴ 70
0
votes
1
reply
282
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
4 months ago
mdidish
▴ 10
0
votes
0
replies
233
views
DiffBind dba.plotprofile y-axis range
DiffBind
4 months ago
Tara
• 0
0
votes
8
replies
728
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
476
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 4 months ago by
Rory Stark
★ 5.2k • written 4 months ago by
jesswhitts
• 0
0
votes
0
replies
365
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
5 months ago
gamma.jian
▴ 10
0
votes
2
replies
444
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
5 months ago
Mallory
• 0
0
votes
0
replies
250
views
Difference in Contrast in DiffBind
DiffBind
7 months ago
user_bioinfo
• 0
0
votes
0
replies
286
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
7 months ago
Dinesh
• 0
0
votes
1
reply
555
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 5 weeks ago by
B.N
• 0 • written 7 months ago by
Henry
▴ 10
0
votes
0
replies
364
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
7 months ago
yvonneh
• 0
0
votes
0
replies
282
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 7 weeks ago
Ian D.
▴ 70
1
vote
1
reply
446
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 7 months ago by
Michael Love
43k • written 7 months ago by
marcusn
• 0
0
votes
1
reply
713
views
ATACseq merge peaks
DiffBind
updated 7 months ago by
ATpoint
★ 4.6k • written 7 months ago by
Shloka
• 0
0
votes
4
replies
560
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 months ago
lonn
• 0
0
votes
0
replies
274
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
8 months ago
Virangika
• 0
2
votes
2
replies
594
views
[DiffBind] Obtaining normalization factors
DiffBind
8 months ago • updated 7 months ago
Henry
▴ 10
2
votes
2
replies
960
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
8 months ago
Henry
▴ 10
0
votes
0
replies
374
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
8 months ago
feather-W
• 0
0
votes
0
replies
371
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
8 months ago
Ankit
▴ 20
0
votes
0
replies
336
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
8 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
368
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 months ago
erbrocato
• 0
0
votes
2
replies
608
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 months ago
Sam
▴ 10
0
votes
1
reply
460
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 months ago • updated 8 months ago
red_bricks
▴ 60
0
votes
1
reply
599
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
10 months ago
isaromero8888
• 0
0
votes
0
replies
619
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
10 months ago
Jawahar
• 0
0
votes
0
replies
366
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
10 months ago
frueher
• 0
0
votes
0
replies
339
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
11 months ago
Aswathy
• 0
0
votes
0
replies
500
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
11 months ago
Hai
• 0
0
votes
0
replies
449
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
11 months ago
inna.gur
• 0
0
votes
1
reply
1.2k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 11 months ago by
qq809825706
• 0 • written 15 months ago by
Mark
• 0
0
votes
2
replies
622
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 12 months ago by
Sam
▴ 10
1
vote
2
replies
548
views
Inconsistent results in DiffBind
DiffBind
12 months ago
Sam
▴ 10
1
vote
1
reply
599
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
635
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
639
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
1.5k
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
669
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
14 months ago
r.murakami
• 0
1
vote
1
reply
774
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 14 months ago by
James W. MacDonald
67k • written 14 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
900
views
diffbind analyze for wheat
DiffBind
updated 9 months ago by
Igor
• 0 • written 15 months ago by
zgyu12
• 0
0
votes
1
reply
833
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
15 months ago
Mark
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Feature Counts - potential bug with outfile.jcounts
by
Gordon Smyth
52k
I agree that the current behavior is not entirely satisfactory and, indeed, it has prevented me from using the junction read counts from fe…
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi Gordon, Sorry, I didn't see the added response to your original answer. I think that would be a great idea; a novel junction to annot…
Comment: Cannot install GO.db and org.Hs.eg.db
by
Gabriel
• 0
The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, …
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
by
Michael Love
43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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