Showing : DiffBind • reset
8
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4
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1.5k
views
How to select summit size for histone ChiP-Seq in Diffbind
Diffbind Histone Chip-Seq Summit size
updated 2 days ago by ★ 3.9k • written 3.8 years ago by ▴ 40
0
votes
2
replies
90
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2 days ago • updated 1 day ago sh.kazempour94 ▴ 10
0
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1
reply
99
views
Hard coding in DiffBind DBA.R line 968
DiffBind
updated 5 days ago by ★ 3.9k • written 8 days ago by ★ 1.2k
0
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1
reply
117
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DiffBind confusions
DiffBind
updated 9 days ago by ★ 3.9k • written 9 days ago by • 0
0
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2
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82
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DiffBind -- Error: No sites have activity greater than minMaxval
DiffBind
10 days ago • updated 9 days ago Alexandre • 0
0
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1
reply
70
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 22 days ago by 57k • written 23 days ago by ▴ 240
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0
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69
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
24 days ago • updated 23 days ago Rory Stark ★ 3.9k
2
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5
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169
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
4 weeks ago ben.vanderveer • 0
2
votes
3
replies
146
views
Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind dba.plotPCA
updated 4 weeks ago by ★ 3.9k • written 5 weeks ago by • 0
1
vote
4
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908
views
DiffBind not accessible files in Example data
diffbind
updated 5 weeks ago by ★ 3.9k • written 3.5 years ago by • 0
0
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4
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207
views
DiffBind
ATACSeq DiFFBind
8 weeks ago • updated 29 days ago Riba Michela ▴ 80
0
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0
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81
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DiffBind reporting error
DiffBind
5 weeks ago Ivan • 0
1
vote
2
replies
665
views
diffBind report Fold scale
diffBind Fold Change
updated 5 weeks ago by • 0 • written 2.4 years ago by • 0
0
votes
4
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307
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
votes
1
reply
130
views
How to retrieve peak summit from DiffBind peaks
DiffBind
updated 7 weeks ago by ★ 3.9k • written 7 weeks ago by • 0
1
vote
2
replies
263
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
10 weeks ago • updated 8 weeks ago mwong043 • 0
2
votes
1
reply
118
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 10 weeks ago by ★ 3.9k • written 10 weeks ago by ▴ 10
2
votes
2
replies
202
views
A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 10 weeks ago by ★ 3.9k • written 12 weeks ago by ▴ 10
0
votes
7
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233
views
DiffBind DEseq
DiffBind
10 weeks ago • updated 9 weeks ago 浩然 • 0
0
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0
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98
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
11 weeks ago Goku • 0
2
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6
replies
238
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
317
views
DiffBind how to retrieve normalized count matrix of ATAC-seq data
DiffBind
updated 10 weeks ago by ★ 3.9k • written 12 weeks ago by ▴ 10
1
vote
1
reply
138
views
diffbind installation through Conda fails
DiffBind conda
updated 12 weeks ago by ★ 3.9k • written 12 weeks ago by ▴ 90
1
vote
5
replies
249
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 12 weeks ago by 57k • written 3 months ago by • 0
0
votes
4
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295
views
How sensitive is DiffBind to Deseq2 assumptions ?
DESeq2 DiffBind
updated 10 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
3 months ago • updated 12 weeks ago fleur_p90 • 0
1
vote
4
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224
views
DiffBind: dba.contrast for interaction terms
DiffBind
updated 10 weeks ago by ★ 3.9k • written 3 months ago by • 0
0
votes
1
reply
117
views
DiffBind with spike in
DiffBind
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
1
vote
2
replies
193
views
Diffbind error while running example data
DiffBind
3 months ago Lucky • 0
1
vote
1
reply
131
views
DiffBind fragmentSize meaning
DiffBind
updated 3 months ago by ★ 3.9k • written 3 months ago by • 0
2
votes
4
replies
214
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
126
views
Diffbind principal components
PCA DiffBind
updated 4 months ago by ★ 3.9k • written 4 months ago by • 0
1
vote
4
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221
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
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455
views
error: DBA object is already formed from a consensus peakset
DiffBind
4 months ago ahua217 ▴ 10
2
votes
2
replies
287
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
145
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
161
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
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450
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
377
views
The compare result is different in score and Conc in DiffBind
DiffBind
4 months ago Guandong Shang ▴ 20
1
vote
4
replies
194
views
DiffBind dba.count error
DiffBind
4 months ago mdidish • 0
1
vote
2
replies
233
views
How does DiffBind deal with single-end and paired-end data together
DiffBind ssss
5 months ago Xiaojie Cheng • 0
0
votes
6
replies
893
views
DiffBind: Error in heights * sapply(called, function(x) x)
diffbind dba.count summits
updated 5 months ago by ★ 3.9k • written 3.5 years ago by • 0
0
votes
3
replies
193
views
Does DiffBind correctly designate peaks with very small fold-change to be statistically significant?
DESeq2 DiffBind
updated 22 days ago by ★ 3.9k • written 5 months ago by ▴ 10
1
vote
8
replies
318
views
DiffBind 'mc.cores' > 1 is not supported on Windows
DiffBind
5 months ago GM ▴ 10
5
votes
6
replies
219
views
Checking/updating package versions
DiffBind
5 months ago bertb • 0
0
votes
1
reply
223
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
752
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
5 months ago • updated 11 weeks ago Sam ▴ 10
0
votes
4
replies
414
views
Bam files causing Blacklist errors in dba.analyze() but not in dba.blacklist()
DiffBind
5 months ago ahua217 ▴ 10
6
votes
8
replies
790
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
513
views
Learning DiffBind - some basic questions
DiffBind
updated 3 months ago by ★ 3.9k • written 5 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 for allele-specific expression with contrasts between conditions by Michael Love 33k
There is a section in the vignette on interactions that will help you here. You want to test for within-individual effects (`allele`) and c…
Answer: Issues with Tximport by Michael Love 33k
Your file has no version numbers, while your `tx2gene` does have version numbers. While the names look similar, they are not a match. tximp…
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w by Michael Love 33k
This is fine and ignorable, it is coming from upstream packages: our use of a TxDb object to pull out transcript to gene mappings.
Comment: DESeq2: NA's in mcols(object)$betaConv by Michael Love 33k
They are actually rounded to zero in the `dds` which requires integer values.
Comment: Reading multiple data segments from FCS 3.0 file by Prashant • 0
If I would like to automate this in a function, is there any way or function that can figure out `ndataset` from the .fcs file directly? I …
Votes
Comment: DESeq2: NA's in mcols(object)$betaConv
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: RUVSeq and Salmon
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