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Diffbind
•
reset
0
votes
2
replies
154
views
ATACseq rudimentary questions
ATACSeq
DiffBind
14 days ago • updated 8 days ago
4747
• 0
1
vote
11
replies
7.5k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.7 years ago by
Oscar
▴ 10
0
votes
0
replies
280
views
DiffBind plot.profile error
BiocParallel
DiffBind
7 months ago
this_is_me_trying
• 0
0
votes
0
replies
1.1k
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
8 months ago
Muhammad
• 0
0
votes
0
replies
388
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
9 months ago
atlanta
• 0
0
votes
4
replies
2.4k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
9 months ago • updated 8 months ago
Mengjun
• 0
0
votes
0
replies
271
views
DiffBind multi-tissue comparison
DiffBind
9 months ago
lryrainche
• 0
1
vote
8
replies
2.8k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
10 months ago • updated 9 months ago
Luca
• 0
0
votes
0
replies
394
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
10 months ago
Harish
• 0
0
votes
4
replies
1.5k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 10 months ago by
Harry
• 0 • written 10 months ago by
tifaGis
• 0
0
votes
1
reply
483
views
building samplesheet and plot profile
DiffBind
11 months ago
yf
• 0
0
votes
5
replies
925
views
Diffbind interpretation of data - fold change
DiffBind
12 months ago
Vera
• 0
0
votes
0
replies
679
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
14 months ago
kim
• 0
0
votes
0
replies
434
views
diffbind covariates
DiffBind
ATACSeq
updated 14 months ago by
Michael Love
43k • written 14 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
1.0k
views
DiffBind dba.report discrepancy
DiffBind
14 months ago
aelbassiouny
• 0
0
votes
0
replies
367
views
DiffBind subset replicates
DiffBind
15 months ago
Haiping
• 0
0
votes
0
replies
670
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
15 months ago
Young Boqin
• 0
0
votes
0
replies
531
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
16 months ago
Alejandro
• 0
0
votes
2
replies
665
views
DiffBind for MBD-seq
MBD-seq
DiffBind
16 months ago
Marianna
▴ 20
0
votes
1
reply
756
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
17 months ago • updated 11 months ago
Ian D.
▴ 70
0
votes
1
reply
650
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
17 months ago
mdidish
▴ 10
0
votes
0
replies
552
views
DiffBind dba.plotprofile y-axis range
DiffBind
17 months ago
Tara
• 0
0
votes
8
replies
1.5k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 17 months ago by
Rory Stark
★ 5.2k • written 17 months ago by
Marianna
▴ 20
1
vote
3
replies
977
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 17 months ago by
Rory Stark
★ 5.2k • written 18 months ago by
jesswhitts
• 0
0
votes
0
replies
847
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
18 months ago
gamma.jian
▴ 10
0
votes
2
replies
1.0k
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
19 months ago
Mallory
• 0
0
votes
0
replies
550
views
Difference in Contrast in DiffBind
DiffBind
20 months ago
user_bioinfo
• 0
0
votes
0
replies
547
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
20 months ago
Dinesh
• 0
0
votes
1
reply
1.1k
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 14 months ago by
B.N
• 0 • written 20 months ago by
Henry
▴ 10
0
votes
0
replies
857
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
20 months ago
yvonneh
• 0
0
votes
0
replies
492
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
20 months ago
Ian D.
▴ 70
0
votes
9
replies
2.0k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
20 months ago • updated 15 months ago
Ian D.
▴ 70
3
votes
1
reply
930
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 20 months ago by
Michael Love
43k • written 20 months ago by
marcusn
▴ 10
0
votes
1
reply
1.4k
views
ATACseq merge peaks
DiffBind
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
Shloka
• 0
0
votes
4
replies
995
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
21 months ago
lonn
• 0
0
votes
0
replies
562
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
21 months ago
Virangika
• 0
2
votes
2
replies
1.1k
views
[DiffBind] Obtaining normalization factors
DiffBind
21 months ago
Henry
▴ 10
2
votes
2
replies
1.9k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
21 months ago
Henry
▴ 10
0
votes
0
replies
670
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
21 months ago
feather-W
• 0
0
votes
0
replies
671
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
21 months ago
Ankit
▴ 20
0
votes
0
replies
659
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
21 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
606
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
22 months ago
erbrocato
• 0
0
votes
2
replies
968
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
22 months ago
Sam
▴ 10
0
votes
1
reply
813
views
Exact same results in Diffbind with different normalization methods
DiffBind
22 months ago
red_bricks
▴ 60
0
votes
1
reply
1.1k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
23 months ago
isaromero8888
• 0
0
votes
0
replies
990
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
24 months ago
Jawahar
• 0
0
votes
0
replies
631
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
24 months ago
frueher
• 0
0
votes
0
replies
576
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
2.0 years ago
Aswathy
• 0
0
votes
0
replies
835
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
2.0 years ago
Hai
• 0
0
votes
0
replies
711
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
2.0 years ago
inna.gur
• 0
679 results • Page
1 of 14
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Comment: Incosistencies in buildSNNGraph() function
by
ATpoint
★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function
by
Aaron Lun
★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops!
by
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• 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub?
by
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• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
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by
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Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
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Answer: Incosistencies in buildSNNGraph() function
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