Showing : Diffbind • reset
0
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4
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dba.count error
DiffBind
updated 6 hours ago by ★ 4.3k • written 1 day ago by • 0
0
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1
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51
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DiffBind issue: zero values for all peaks in one chromosome
DiffBind
updated 7 days ago by ★ 4.3k • written 8 days ago by • 0
1
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6
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261
views
DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
DiffBind dba.count
updated 5 hours ago by ★ 4.3k • written 14 days ago by • 0
3
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9
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1.1k
views
How to get all possible comparisons in DiffBind
diffbind
updated 9 days ago by ★ 4.3k • written 3.1 years ago by • 0
2
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3
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145
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Not able to replicated Diffbind example dataset.
DiffBind
13 days ago • updated 10 days ago Ayyappa • 0
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0
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44
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Not able to replicated Diffbind example dataset.
DiffBind
13 days ago Ayyappa • 0
1
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10
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343
views
DiffBind: Values of Called1 and Called2 do not appear to coincide with input peaks
DiffBind
updated 9 days ago by ★ 4.3k • written 17 days ago by • 0
1
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1
reply
147
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 5 weeks ago by ★ 4.3k • written 6 weeks ago by • 0
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3
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460
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DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 6 weeks ago by • 0 • written 6 months ago by • 0
0
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1
reply
181
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 5 weeks ago by • 0 • written 7 weeks ago by • 0
0
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1
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146
views
diffbind binding affinity matrix
diffbind DiffBind
updated 7 weeks ago by ★ 4.3k • written 10 weeks ago by • 0
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1
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255
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DiffBind bUseSummarizeOverlaps error - the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExper…
DiffBind ChIPSeqData
updated 7 weeks ago by ★ 4.3k • written 8 weeks ago by • 0
3
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4
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215
views
dba.contrast in DiffBind
v3.4.0 DiffBind
updated 7 weeks ago by ★ 4.3k • written 8 weeks ago by • 0
1
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2
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178
views
How to include/show/add correction factors/numbers to the Diffbind heat map tiles
DiffBind
updated 11 weeks ago by ▴ 40 • written 11 weeks ago by • 0
3
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4
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1.0k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 3 months ago by ▴ 10 • written 3.5 years ago by ▴ 10
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0
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115
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3 months ago Drew • 0
1
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2
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208
views
DiffBind in Bioconda
DiffBind Bioconda Versions
4 months ago • updated 3 months ago Riba Michela ▴ 90
0
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0
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104
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DiffBind dba.counts memory issue
DiffBind
3 months ago rreese2 • 0
0
votes
2
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215
views
how to select specific genes from heatmap of differentially accessible regions of ATAC-seq in DiffBind
DiffBind
updated 3 months ago by ★ 4.3k • written 4 months ago by • 0
0
votes
1
reply
192
views
Can DiffBind do differential analysis for un-paired peaksets?
DiffBind
updated 4 months ago by ★ 4.3k • written 4 months ago by • 0
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2
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334
views
Diffbind dba.plotProfile attempt to select less than one element in OneIndex
DiffBind
4 months ago bhanratt • 0
0
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3
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268
views
DiifBind_DBA_report
DiffBind
updated 7 weeks ago by ★ 4.3k • written 4 months ago by ▴ 90
2
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1
reply
242
views
Diffbind: differences between design vs no design (same comparison)?
DiffBind
updated 4 months ago by ★ 4.3k • written 4 months ago by • 0
1
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2
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207
views
DiffBind fold parameter vs. IfcThreshold in DESeq2
DiffBind
5 months ago • updated 4 months ago Shuwan ▴ 10
3
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4
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331
views
DiffBind (Error in if (DBA$config$parallelPackage))
parallel R DiffBind
updated 7 weeks ago by ★ 4.3k • written 5 months ago by • 0
0
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3
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188
views
DiffBind Occupancy analysis
DiffBind
updated 5 months ago by ★ 4.3k • written 5 months ago by • 0
0
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3
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291
views
issue with DiffBind dba.count
bam bai DiffBind dba.count Diffbind
updated 5 months ago by ★ 4.3k • written 5 months ago by • 0
0
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0
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103
views
Diffbind issue
DiffBind
5 months ago mtsompana • 0
3
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12
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822
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 5 months ago by ★ 4.3k • written 2.4 years ago by ▴ 20
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0
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158
views
DiffBind error during normalization
DiffBind
5 months ago jseg ▴ 10
0
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2
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214
views
DiffBind
bflip dba.report DiffBind
6 months ago • updated 5 months ago Riba Michela ▴ 90
2
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3
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331
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4 months ago by ▴ 20 • written 6 months ago by • 0
1
vote
3
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294
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 6 months ago by ▴ 70 • written 6 months ago by • 0
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0
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146
views
Diffbind without replicates
DiffBind
6 months ago Danielle • 0
5
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7
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536
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
6 months ago pegah.taklifi ▴ 30
0
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1
reply
174
views
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
DESeq2 Diffbind
updated 6 months ago by ★ 4.3k • written 6 months ago by • 0
1
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2
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219
views
Output of normalizing a dba object with DBA_DESEQ2,normalize = DBA_NORM_RLE in Diffbind
DiffBind
6 months ago Alexandre • 0
0
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0
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171
views
Are broad/narrow peak comparable?
Peaks MAC2 DiffBind
6 months ago Yuan Tian ▴ 240
0
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0
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149
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Interpretation of diffbind coefficients
DiffBind
6 months ago Alexandre • 0
1
vote
2
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223
views
DiffBind dba.report(): Question about DBA_ALL_METHODS
DiffBind
6 months ago etiennedanis • 0
1
vote
1
reply
164
views
How are greylists derived in DiffBind
DiffBind
updated 7 months ago by ★ 4.3k • written 7 months ago by • 0
2
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1
reply
405
views
DiffBind Error in if (file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed
DiffBind
updated 7 months ago by ★ 4.3k • written 7 months ago by • 0
0
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1
reply
217
views
DiffBind normalisation factor retrieval
edgeR Normalization DiffBind
updated 7 months ago by ★ 4.3k • written 7 months ago by • 0
9
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4
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2.1k
views
How to select summit size for histone ChiP-Seq in Diffbind
Diffbind Histone Chip-Seq Summit size
updated 7 months ago by ★ 4.3k • written 4.4 years ago by ▴ 40
1
vote
4
replies
444
views
Binding matrix created by DiffBind
ATACSeq DiffBind
7 months ago sh.kazempour94 ▴ 10
0
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1
reply
228
views
Hard coding in DiffBind DBA.R line 968
DiffBind
updated 7 months ago by ★ 4.3k • written 7 months ago by ★ 1.3k
0
votes
1
reply
373
views
DiffBind confusions
DiffBind
updated 7 months ago by ★ 4.3k • written 7 months ago by • 0
2
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7
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481
views
DiffBind -- Error: No sites have activity greater than minMaxval
DiffBind
updated 6 months ago by ★ 4.3k • written 7 months ago by • 0
0
votes
1
reply
424
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 8 months ago by 58k • written 8 months ago by ▴ 240
1
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2
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543
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
8 months ago • updated 4 months ago Rory Stark ★ 4.3k
50 results • Page 1 of 1
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Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
Comment: Unable to install Rhtslib in R-4.1.1 by cf2209 • 0
Thank you for your input I appreciate it. I will revise and make changes to this post as you suggested. Unfortunately I am not able to do t…
Votes
Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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