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DiFFBind
•
reset
0
votes
7
replies
2.1k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 22 months ago by
Oscar
• 0
0
votes
1
reply
111
views
building samplesheet and plot profile
DiffBind
21 days ago • updated 19 days ago
yf
• 0
0
votes
5
replies
314
views
Diffbind interpretation of data - fold change
DiffBind
6 weeks ago
Vera
• 0
0
votes
0
replies
260
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
3 months ago
kim
• 0
0
votes
0
replies
194
views
diffbind covariates
DiffBind
ATACSeq
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
582
views
DiffBind dba.report discrepancy
DiffBind
4 months ago
aelbassiouny
• 0
0
votes
0
replies
135
views
DiffBind subset replicates
DiffBind
4 months ago
Haiping
• 0
0
votes
0
replies
248
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
4 months ago
Young Boqin
• 0
0
votes
0
replies
270
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
5 months ago
Alejandro
• 0
0
votes
2
replies
411
views
DiffBind for MBD-seq
MBD-seq
DiffBind
5 months ago
Marianna
▴ 20
0
votes
1
reply
469
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
6 months ago • updated 10 days ago
Ian D.
▴ 70
0
votes
1
reply
350
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
6 months ago
mdidish
▴ 10
0
votes
0
replies
287
views
DiffBind dba.plotprofile y-axis range
DiffBind
6 months ago
Tara
• 0
0
votes
8
replies
840
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 6 months ago by
Rory Stark
★ 5.2k • written 6 months ago by
Marianna
▴ 20
1
vote
3
replies
569
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 7 months ago by
Rory Stark
★ 5.2k • written 7 months ago by
jesswhitts
• 0
0
votes
0
replies
439
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
7 months ago
gamma.jian
▴ 10
0
votes
2
replies
542
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
8 months ago
Mallory
• 0
0
votes
0
replies
303
views
Difference in Contrast in DiffBind
DiffBind
9 months ago
user_bioinfo
• 0
0
votes
0
replies
333
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
9 months ago
Dinesh
• 0
0
votes
1
reply
651
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 3 months ago by
B.N
• 0 • written 9 months ago by
Henry
▴ 10
0
votes
0
replies
440
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
9 months ago
yvonneh
• 0
0
votes
0
replies
323
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
9 months ago
Ian D.
▴ 70
0
votes
9
replies
1.4k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
9 months ago • updated 4 months ago
Ian D.
▴ 70
3
votes
1
reply
586
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 9 months ago by
Michael Love
43k • written 9 months ago by
marcusn
▴ 10
0
votes
1
reply
895
views
ATACseq merge peaks
DiffBind
updated 10 months ago by
ATpoint
★ 4.7k • written 10 months ago by
Shloka
• 0
0
votes
4
replies
629
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
10 months ago
lonn
• 0
0
votes
0
replies
333
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
10 months ago
Virangika
• 0
2
votes
2
replies
715
views
[DiffBind] Obtaining normalization factors
DiffBind
10 months ago
Henry
▴ 10
2
votes
2
replies
1.2k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
10 months ago
Henry
▴ 10
0
votes
0
replies
423
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
10 months ago
feather-W
• 0
0
votes
0
replies
455
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
10 months ago
Ankit
▴ 20
0
votes
0
replies
400
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
10 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
418
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
11 months ago
erbrocato
• 0
0
votes
2
replies
680
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
11 months ago
Sam
▴ 10
0
votes
1
reply
513
views
Exact same results in Diffbind with different normalization methods
DiffBind
11 months ago
red_bricks
▴ 60
0
votes
1
reply
705
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
13 months ago
isaromero8888
• 0
0
votes
0
replies
702
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
13 months ago
Jawahar
• 0
0
votes
0
replies
416
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
13 months ago
frueher
• 0
0
votes
0
replies
391
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
13 months ago
Aswathy
• 0
0
votes
0
replies
559
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
13 months ago
Hai
• 0
0
votes
0
replies
496
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
13 months ago
inna.gur
• 0
0
votes
1
reply
1.3k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 13 months ago by
qq809825706
• 0 • written 18 months ago by
Mark
• 0
0
votes
2
replies
706
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 14 months ago by
Sam
▴ 10
1
vote
2
replies
605
views
Inconsistent results in DiffBind
DiffBind
14 months ago
Sam
▴ 10
1
vote
1
reply
659
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 14 months ago by
ATpoint
★ 4.7k • written 14 months ago by
Miquel
• 0
0
votes
0
replies
702
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
15 months ago
jared.andrews07
▴ 30
0
votes
0
replies
713
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 16 months ago by
James W. MacDonald
68k • written 16 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 16 months ago by
Matt Eldridge
▴ 10 • written 16 months ago by
r.murakami
• 0
2
votes
2
replies
729
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
16 months ago
r.murakami
• 0
1
vote
1
reply
866
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
lin.pei26
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: normalizatino of dna methylation EPIC data
by
user_bioinfo
• 0
yes actually that's why I did, and its all good! thank you for your response
Comment: batch effect removal for agilent microarray data
by
gaye.yilmaz
• 0
Hello again, Can using inSilicoMerging handle this situation?
Answer: normalizatino of dna methylation EPIC data
by
James W. MacDonald
68k
Your code doesn't show the error? Anyway, the default for `colMeans2` is useNames = TRUE, and the call to `colMeans2` in `preprocessNoob…
Answer: WGCNA
by
James W. MacDonald
68k
This support site is meant to help people with technical questions about using Bioconductor packages, rather than as a place to get analysi…
Answer: EuroBioC2023 abstract submission is open!
by
cirwin009
• 0
Submit here https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/ [Block Blast][1] This article offers a thorough and in-depth…
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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user_bioinfo
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Michael Love
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