Showing : DiffBind • reset
2
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6
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143
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Interpret plot from DiffBind
DiffBind
7 days ago • updated 1 hour ago Chris • 0
0
votes
0
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23
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Title in dba.plotProfile
DiffBind
2 days ago agata17 • 0
0
votes
1
reply
97
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dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 8 days ago by ★ 4.9k • written 15 days ago by ▴ 10
0
votes
1
reply
140
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DiffBind dba() in parallel
DiffBind
updated 8 days ago by ★ 4.9k • written 9 days ago by • 0
1
vote
4
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219
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 12 hours ago by ★ 4.9k • written 9 days ago by • 0
0
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0
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48
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Fold values in Diffbind
DiffBind
9 days ago bhandary.8590 • 0
0
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3
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167
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 10 days ago by • 0
0
votes
0
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99
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Help with Diffbind result
DiffBind
17 days ago Chris • 0
3
votes
4
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277
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
24 days ago Mark • 0
0
votes
7
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445
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DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
6 weeks ago • updated 2 days ago Ti • 0
2
votes
1
reply
151
views
how diffbind count the reads of each peak in each sample?
diffbind DiffBind
updated 6 weeks ago by ★ 4.9k • written 6 weeks ago by • 0
0
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5
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337
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DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 25 days ago by • 0 • written 6 weeks ago by • 0
3
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6
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283
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Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
6 weeks ago Chris • 0
0
votes
1
reply
179
views
Plotting read densities from DiffBind results
Read density DiffBind
updated 7 weeks ago by ★ 4.9k • written 8 weeks ago by • 0
0
votes
2
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183
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Question regarding multiple comparisons in DiffBind
DiffBind
8 weeks ago • updated 6 weeks ago epipally • 0
7
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13
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724
views
Help with Error in DiffBind
DiffBind ATACSeq
10 weeks ago • updated 8 weeks ago Chris • 0
0
votes
2
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224
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 9 weeks ago by ★ 4.9k • written 9 weeks ago by • 0
0
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2
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272
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
10 weeks ago Giulia • 0
0
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0
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96
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
10 weeks ago Giulia • 0
1
vote
3
replies
178
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 11 weeks ago by ★ 4.9k • written 11 weeks ago by • 0
1
vote
2
replies
174
views
DiffBind spike-in lib.sizes confusion
SpikeIn DiffBind
12 weeks ago • updated 11 weeks ago Weisheng • 0
0
votes
13
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542
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze DiffBind @rory-stark-5741
11 weeks ago • updated 9 weeks ago tahir.msajid • 0
0
votes
1
reply
132
views
DiffBind---peak region reads or all reads？
DiffBind
updated 11 weeks ago by ★ 4.9k • written 3 months ago by • 0
0
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0
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86
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind MeRIP-seq m6A-seq
12 weeks ago zhiyi • 0
0
votes
1
reply
200
views
DiffBind differential analysis
DifferentialPeakCalling ChIPanalyser DiffBind chipseqDB
updated 3 months ago by ★ 4.9k • written 3 months ago by • 0
1
vote
3
replies
358
views
DiffBind---Normalization problem-spike in or no spike in beforehand?
DiffBind
updated 3 months ago by ★ 4.9k • written 3 months ago by • 0
0
votes
1
reply
182
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 3 months ago by ★ 4.9k • written 4 months ago by • 0
0
votes
1
reply
186
views
Setting DBA$config$mergeOverlap for Diffbind
DiffBind
updated 3 months ago by ★ 4.9k • written 3 months ago by • 0
0
votes
2
replies
255
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 4 months ago by ★ 4.9k • written 4 months ago by • 0
0
votes
7
replies
504
views
Issue in generating a new DBA object with custom counts
DiffBind dbaobject
5 months ago • updated 4 months ago francesco.gandolfi • 0
0
votes
1
reply
245
views
Diffbind matrix/batch effect/normalization
DiffBind
updated 4 months ago by ★ 4.9k • written 6 months ago by ▴ 10
0
votes
8
replies
454
views
Question about Diffbind counts
DiffBind
4 months ago slrpatty • 0
0
votes
3
replies
402
views
Minor issue regarding customization of text size in Volcano and Heatmap Plots
DiffBind
updated 4 months ago by ★ 4.9k • written 5 months ago by ▴ 10
0
votes
1
reply
190
views
dba.count Error in DiffBind
DiffBind
4 months ago narzouni • 0
3
votes
4
replies
580
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
5 months ago • updated 4 months ago spg • 0
0
votes
1
reply
366
views
DiffBind: Error in pv$called[, mask] : subscript out of bounds
DiffBind
updated 5 months ago by ★ 4.9k • written 6 months ago by • 0
1
vote
2
replies
246
views
DiffBind Loss and Gain location
DiffBind
updated 4 months ago by ★ 4.9k • written 5 months ago by • 0
0
votes
2
replies
351
views
Blacklist error in DiffBind
DiffBind Blacklist
6 months ago Romain • 0
2
votes
1
reply
342
views
Error in DiffBind dba.blacklist & dba.count
DiffBind
updated 6 months ago by ★ 4.9k • written 6 months ago by • 0
2
votes
1
reply
316
views
Different sequencing depth between replicates and samples
DESeq2 edgeR DiffBind
updated 7 months ago by 47k • written 7 months ago by ▴ 10
2
votes
12
replies
899
views
Too much data for Diffbind
DiffBind
7 months ago littlefishes20 ▴ 10
2
votes
4
replies
503
views
DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 6 months ago by ★ 4.9k • written 7 months ago by ▴ 660
1
vote
25
replies
1.6k
views
DiffBind spike-in normalization
DiffBind
7 months ago yuhuihui2011 • 0
0
votes
1
reply
389
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
2
votes
4
replies
824
views
Normalizing Cut&Tag peak data
Normalization Peakdata DiffBind Cut&Tag
updated 7 months ago by ★ 2.9k • written 8 months ago by • 0
0
votes
3
replies
394
views
Issue carrying out DiffBind Analysis at a predefined peak set
DiffBind
updated 7 months ago by ★ 4.9k • written 8 months ago by • 0
2
votes
1
reply
934
views
DiffBind: Error in if (res$config$bCorPlot) { : the condition has length > 1
DiffBind ChIPQC
updated 8 months ago by ★ 4.9k • written 9 months ago by • 0
0
votes
7
replies
1.1k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 9 months ago by ▴ 40 • written 3.1 years ago by ▴ 10
1
vote
2
replies
444
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
10 months ago etiennedanis • 0
0
votes
2
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552
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DESeq2 analysis has not been run for this contrast
R DiffBind
10 months ago Wang • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind by Chris • 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind by Chris • 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting by phelankj • 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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