Showing : diffBind • reset
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25
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Binding matrix created by DiffBind
ATACSeq DiffBind
16 hours ago • updated 15 hours ago sh.kazempour94 ▴ 10
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1
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88
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Hard coding in DiffBind DBA.R line 968
DiffBind
updated 2 days ago by ★ 3.9k • written 5 days ago by ★ 1.2k
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1
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100
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DiffBind confusions
DiffBind
updated 7 days ago by ★ 3.9k • written 7 days ago by • 0
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2
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81
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DiffBind -- Error: No sites have activity greater than minMaxval
DiffBind
8 days ago • updated 7 days ago Alexandre • 0
0
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1
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67
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 20 days ago by 57k • written 20 days ago by ▴ 240
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
22 days ago • updated 20 days ago Rory Stark ★ 3.9k
2
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5
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167
views
erorr in normalization with DiffBind: pv$binding[, colnum] <- pv$peaks[[i]]$RPKM: number of items to replace is not a multiple of replacement length
DiffBind
29 days ago • updated 28 days ago ben.vanderveer • 0
2
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3
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145
views
Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind dba.plotPCA
updated 4 weeks ago by ★ 3.9k • written 4 weeks ago by • 0
1
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4
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905
views
DiffBind not accessible files in Example data
diffbind
updated 4 weeks ago by ★ 3.9k • written 3.5 years ago by • 0
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4
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203
views
DiffBind
ATACSeq DiFFBind
7 weeks ago • updated 27 days ago Riba Michela ▴ 80
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0
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80
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DiffBind reporting error
DiffBind
5 weeks ago Ivan • 0
1
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2
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662
views
diffBind report Fold scale
diffBind Fold Change
updated 5 weeks ago by • 0 • written 2.4 years ago by • 0
0
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4
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306
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 5 weeks ago by ★ 3.9k • written 21 months ago by ▴ 20
2
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1
reply
129
views
How to retrieve peak summit from DiffBind peaks
DiffBind
updated 6 weeks ago by ★ 3.9k • written 6 weeks ago by • 0
1
vote
2
replies
259
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
10 weeks ago • updated 8 weeks ago mwong043 • 0
2
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1
reply
117
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 9 weeks ago by ★ 3.9k • written 10 weeks ago by ▴ 10
2
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2
replies
200
views
A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 9 weeks ago by ★ 3.9k • written 12 weeks ago by ▴ 10
0
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7
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232
views
DiffBind DEseq
DiffBind
10 weeks ago • updated 9 weeks ago 浩然 • 0
0
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0
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96
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
11 weeks ago Goku • 0
2
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6
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237
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
12 weeks ago • updated 11 weeks ago Goku • 0
4
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7
replies
314
views
DiffBind how to retrieve normalized count matrix of ATAC-seq data
DiffBind
updated 9 weeks ago by ★ 3.9k • written 12 weeks ago by ▴ 10
1
vote
1
reply
132
views
diffbind installation through Conda fails
DiffBind conda
updated 11 weeks ago by ★ 3.9k • written 12 weeks ago by ▴ 90
1
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5
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245
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How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 11 weeks ago by 57k • written 12 weeks ago by • 0
0
votes
4
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290
views
How sensitive is DiffBind to Deseq2 assumptions ?
DESeq2 DiffBind
updated 9 weeks ago by ★ 3.9k • written 12 weeks ago by ▴ 10
1
vote
3
replies
182
views
DiffBind: bGain or bLoss parameters in dba.report don't work?
DiffBind
12 weeks ago fleur_p90 • 0
1
vote
4
replies
222
views
DiffBind: dba.contrast for interaction terms
DiffBind
updated 9 weeks ago by ★ 3.9k • written 12 weeks ago by • 0
0
votes
1
reply
115
views
DiffBind with spike in
DiffBind
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
1
vote
2
replies
191
views
Diffbind error while running example data
DiffBind
3 months ago Lucky • 0
1
vote
1
reply
127
views
DiffBind fragmentSize meaning
DiffBind
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
2
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4
replies
211
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
1
vote
1
reply
123
views
Diffbind principal components
PCA DiffBind
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
1
vote
4
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220
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
4 months ago • updated 3 months ago SFn • 0
1
vote
14
replies
450
views
error: DBA object is already formed from a consensus peakset
DiffBind
4 months ago ahua217 ▴ 10
2
votes
2
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286
views
DiffBind installation fails: Error: package ‘BiocGenerics’ 0.34.0 is loaded, but >= 0.36.0 is required by ‘IRanges’
systemPipeR Bioconductor DiffBind BiocGenerics
updated 4 months ago by 25k • written 4 months ago by • 0
1
vote
1
reply
144
views
dba.count() of DiffBind 3.0 does not have bSubControl parameter
DiffBind
updated 4 months ago by ★ 3.9k • written 4 months ago by • 0
1
vote
2
replies
160
views
How to make BiocParallel work in DiffBind when working under windows system
DiffBind
updated 4 months ago by 25k • written 4 months ago by ▴ 20
1
vote
7
replies
449
views
Conc_1 in differnet dba.report result is slightly different
DiffBind
updated 4 months ago by ★ 3.9k • written 5 months ago by ▴ 20
1
vote
8
replies
376
views
The compare result is different in score and Conc in DiffBind
DiffBind
4 months ago Guandong Shang ▴ 20
1
vote
4
replies
192
views
DiffBind dba.count error
DiffBind
4 months ago mdidish • 0
1
vote
2
replies
231
views
How does DiffBind deal with single-end and paired-end data together
DiffBind ssss
5 months ago • updated 4 months ago Xiaojie Cheng • 0
0
votes
6
replies
883
views
DiffBind: Error in heights * sapply(called, function(x) x)
diffbind dba.count summits
updated 4 months ago by ★ 3.9k • written 3.5 years ago by • 0
0
votes
3
replies
191
views
Does DiffBind correctly designate peaks with very small fold-change to be statistically significant?
DESeq2 DiffBind
updated 19 days ago by ★ 3.9k • written 5 months ago by ▴ 10
1
vote
8
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317
views
DiffBind 'mc.cores' > 1 is not supported on Windows
DiffBind
5 months ago GM ▴ 10
5
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6
replies
216
views
Checking/updating package versions
DiffBind
5 months ago bertb • 0
0
votes
1
reply
219
views
DiffBind error with background=TRUE in dba.normalize?
BiocParallel DiffBind parallel
updated 5 months ago by ★ 3.9k • written 5 months ago by • 0
7
votes
17
replies
748
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
5 months ago • updated 10 weeks ago Sam ▴ 10
0
votes
4
replies
400
views
Bam files causing Blacklist errors in dba.analyze() but not in dba.blacklist()
DiffBind
5 months ago ahua217 ▴ 10
6
votes
8
replies
786
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 5 months ago by • 0 • written 3.6 years ago by ▴ 60
5
votes
10
replies
509
views
Learning DiffBind - some basic questions
DiffBind
updated 12 weeks ago by ★ 3.9k • written 5 months ago by ▴ 10
2
votes
1
reply
133
views
Bewildering PCA plot at DiffBind
DiffBind
updated 5 months ago by ★ 3.9k • written 5 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: New annotation package - no response from packages@bioconductor.org by shepherl 2.7k
I would make sure you are registered and are following the name of the package as a watched tag here on the support site so that if questio…
Comment: New annotation package - no response from packages@bioconductor.org by athief ▴ 10
Thanks for the update. Anything I shall do/prepare in the meantime?
Comment: New annotation package - no response from packages@bioconductor.org by shepherl 2.7k
As an update. We are still working on branching annotations from the recent Bioconductor release. We should have this available within the…
Comment: installing older versions of packages by zuljiamel1991 • 0
That works when specific Bioconductor version is needed. However, within the same version of Bioconductor, few versions of packages are rel…
Comment: installing older versions of packages by zuljiamel1991 • 0
I will check this one, thank you!
Votes
Comment: New annotation package - no response from packages@bioconductor.org
Comment: How to do annotation with Limma
Answer: No counts, just fold change data
How to select summit size for histone ChiP-Seq in Diffbind
A: How to select summit size for histone ChiP-Seq in Diffbind
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