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diffbind
•
reset
1
vote
10
replies
6.2k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 5 weeks ago by
nlp97204
• 0 • written 2.4 years ago by
Oscar
▴ 10
0
votes
0
replies
155
views
DiffBind plot.profile error
BiocParallel
DiffBind
3 months ago
this_is_me_trying
• 0
0
votes
0
replies
894
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
3 months ago
Muhammad
• 0
0
votes
0
replies
286
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
4 months ago
atlanta
• 0
0
votes
4
replies
2.2k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
5 months ago • updated 4 months ago
Mengjun
• 0
0
votes
0
replies
177
views
DiffBind multi-tissue comparison
DiffBind
5 months ago
lryrainche
• 0
1
vote
8
replies
2.6k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
5 months ago
Luca
• 0
0
votes
0
replies
293
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
6 months ago
Harish
• 0
0
votes
4
replies
1.3k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 6 months ago by
Harry
• 0 • written 6 months ago by
tifaGis
• 0
0
votes
1
reply
278
views
building samplesheet and plot profile
DiffBind
7 months ago
yf
• 0
0
votes
5
replies
682
views
Diffbind interpretation of data - fold change
DiffBind
8 months ago
Vera
• 0
0
votes
0
replies
505
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
10 months ago
kim
• 0
0
votes
0
replies
329
views
diffbind covariates
DiffBind
ATACSeq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
870
views
DiffBind dba.report discrepancy
DiffBind
10 months ago
aelbassiouny
• 0
0
votes
0
replies
269
views
DiffBind subset replicates
DiffBind
10 months ago
Haiping
• 0
0
votes
0
replies
514
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
11 months ago
Young Boqin
• 0
0
votes
0
replies
435
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
11 months ago
Alejandro
• 0
0
votes
2
replies
566
views
DiffBind for MBD-seq
MBD-seq
DiffBind
12 months ago
Marianna
▴ 20
0
votes
1
reply
656
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
12 months ago • updated 6 months ago
Ian D.
▴ 70
0
votes
1
reply
510
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
13 months ago • updated 12 months ago
mdidish
▴ 10
0
votes
0
replies
434
views
DiffBind dba.plotprofile y-axis range
DiffBind
13 months ago
Tara
• 0
0
votes
8
replies
1.2k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 13 months ago by
Rory Stark
★ 5.2k • written 13 months ago by
Marianna
▴ 20
1
vote
3
replies
833
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 13 months ago by
Rory Stark
★ 5.2k • written 13 months ago by
jesswhitts
• 0
0
votes
0
replies
634
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
14 months ago
gamma.jian
▴ 10
0
votes
2
replies
858
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
14 months ago
Mallory
• 0
0
votes
0
replies
460
views
Difference in Contrast in DiffBind
DiffBind
16 months ago
user_bioinfo
• 0
0
votes
0
replies
461
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
16 months ago
Dinesh
• 0
0
votes
1
reply
947
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 10 months ago by
B.N
• 0 • written 16 months ago by
Henry
▴ 10
0
votes
0
replies
671
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
16 months ago
yvonneh
• 0
0
votes
0
replies
432
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
16 months ago
Ian D.
▴ 70
0
votes
9
replies
1.7k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
16 months ago • updated 10 months ago
Ian D.
▴ 70
3
votes
1
reply
818
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 16 months ago by
Michael Love
43k • written 16 months ago by
marcusn
▴ 10
0
votes
1
reply
1.2k
views
ATACseq merge peaks
DiffBind
updated 16 months ago by
ATpoint
★ 4.9k • written 16 months ago by
Shloka
• 0
0
votes
4
replies
875
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
16 months ago
lonn
• 0
0
votes
0
replies
484
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
16 months ago
Virangika
• 0
2
votes
2
replies
979
views
[DiffBind] Obtaining normalization factors
DiffBind
17 months ago • updated 16 months ago
Henry
▴ 10
2
votes
2
replies
1.6k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
17 months ago
Henry
▴ 10
0
votes
0
replies
547
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
17 months ago
feather-W
• 0
0
votes
0
replies
588
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
17 months ago
Ankit
▴ 20
0
votes
0
replies
550
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
17 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
537
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
17 months ago
erbrocato
• 0
0
votes
2
replies
836
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
18 months ago
Sam
▴ 10
0
votes
1
reply
674
views
Exact same results in Diffbind with different normalization methods
DiffBind
18 months ago • updated 17 months ago
red_bricks
▴ 60
0
votes
1
reply
912
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
19 months ago
isaromero8888
• 0
0
votes
0
replies
891
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
19 months ago
Jawahar
• 0
0
votes
0
replies
535
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
19 months ago
frueher
• 0
0
votes
0
replies
505
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
20 months ago
Aswathy
• 0
0
votes
0
replies
742
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
20 months ago
Hai
• 0
0
votes
0
replies
624
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
20 months ago
inna.gur
• 0
2
votes
2
replies
1.9k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by
etiennedanis
• 0 • written 2.0 years ago by
Mark
▴ 10
678 results • Page
1 of 14
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Replies
Comment: org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
by
thundernight
• 0
I'm actually having the same problem. [Spanish dictionary][1] [1]: https://spanishdictionary.cc
Comment: voomLmFit fitted log-CPM values
by
Gordon Smyth
53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values
by
Lina
▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values
by
Gordon Smyth
53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Comment: EuroBioC2024 abstract submission is open!
by
Finnianfly
• 0
What specific requirements should be noted when preparing abstracts for presentation formats such as short talks, package demos, or posters…
Votes
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
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