Showing : DiffBind • reset
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2
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Low Differentially Bound Sites found with DiffBind
Cut&Run DiffBind
1 day ago • updated 23 hours ago gannoncottone • 0
0
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1
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66
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 1 day ago by ★ 4.4k • written 16 days ago by • 0
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1
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48
views
DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
DiffBind
updated 1 day ago by ★ 4.4k • written 13 days ago by ▴ 10
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1
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68
views
During dba(sampleSheet = "samples.csv") step, Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=charac…
DiffBind
updated 1 day ago by ★ 4.4k • written 7 days ago by • 0
4
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9
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1.2k
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DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 14 days ago by ▴ 10 • written 11 months ago by ▴ 10
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2
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855
views
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 14 days ago by ▴ 10 • written 7 months ago by • 0
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37
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diffbind dba.report
diffbind
14 days ago jonathanho1989 • 0
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57
views
diffbind dba.count error
peakfiles diffbind HMMRATAC
23 days ago jonathanho1989 • 0
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0
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58
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Diffbind not calling sites as differentially bound
DiffBind
28 days ago • updated 27 days ago ipsc-jl • 0
5
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8
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776
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 27 days ago by ▴ 20 • written 11 months ago by ▴ 30
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1
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109
views
Diffbind: different results on the same sample depending on contrast parameters
DifferentialExpression DiffBind
updated 29 days ago by ★ 4.4k • written 6 weeks ago by • 0
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0
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66
views
How to set $control.subtract to FALSE in DiffBind?
DiffBind
5 weeks ago ksong ▴ 10
2
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3
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196
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
10 weeks ago • updated 6 weeks ago bers.anthrope • 0
2
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5
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182
views
Diffbind dba$binding slot finding Chr21 for an MM10 dataset
DiffBind
updated 7 weeks ago by • 0 • written 7 weeks ago by • 0
0
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3
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161
views
DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change introduced between version 2.14 and 3.4.11
DiffBind
updated 7 weeks ago by ★ 4.4k • written 7 weeks ago by • 0
0
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3
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135
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 7 weeks ago by ★ 4.4k • written 8 weeks ago by • 0
2
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7
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541
views
can the counts extracted from Diffbind be used to analysis in Deseq2 as the RNAseq?
deseq2 diffbind
updated 7 weeks ago by ★ 4.4k • written 22 months ago by • 0
9
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6
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2.5k
views
How to select summit size for histone ChiP-Seq in Diffbind
Diffbind Histone Chip-Seq Summit size
updated 7 weeks ago by ★ 4.4k • written 4.8 years ago by ▴ 40
0
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1
reply
176
views
DiffBind contrast design - pairwise with independent filtering
DiffBind
updated 8 weeks ago by • 0 • written 3 months ago by • 0
0
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1
reply
181
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 3 months ago by ★ 4.4k • written 3 months ago by • 0
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0
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109
views
DiffBind does not load samples
DiffBind
3 months ago nw416 • 0
3
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5
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696
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Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind dba.plotPCA
updated 3 months ago by ★ 4.4k • written 14 months ago by ▴ 10
1
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1
reply
199
views
DiffBind drop out some peaks
DiffBind
updated 3 months ago by ★ 4.4k • written 3 months ago by • 0
0
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0
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114
views
Creating a consensus peakset in DiffBind for all the conditions of an experiment
DiffBind
3 months ago Sam ▴ 10
1
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2
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289
views
BiocParallel error when running DiffBind
BiocParallel BiocPa DiffBind
updated 3 months ago by 25k • written 4 months ago by ▴ 10
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0
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135
views
DiffBind error
DiffBind DifferentialPeakCalling
3 months ago Amandeep • 0
0
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9
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1.1k
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
19 months ago • updated 4 months ago Tongjun • 0
5
votes
6
replies
381
views
How to get 3/4 peak overlap in DiffBind?
DiffBind
5 months ago • updated 4 months ago Krista • 0
3
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11
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1.5k
views
How to get all possible comparisons in DiffBind
diffbind
updated 5 months ago by ★ 4.4k • written 3.5 years ago by • 0
0
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2
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380
views
dba.count() error when re-centering peaks
DiffBind
5 months ago Mark • 0
0
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2
replies
218
views
`dbs.all` object in the vignette
DiffBind
5 months ago Mark • 0
1
vote
6
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593
views
dba.count error
DiffBind
updated 5 months ago by ★ 4.4k • written 5 months ago by ▴ 10
1
vote
6
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491
views
DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
DiffBind dba.count
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
0
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1
reply
135
views
DiffBind issue: zero values for all peaks in one chromosome
DiffBind
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
8
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20
replies
2.0k
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
updated 5 months ago by ★ 4.4k • written 18 months ago by ▴ 10
1
vote
10
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581
views
DiffBind: Values of Called1 and Called2 do not appear to coincide with input peaks
DiffBind
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
2
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3
replies
290
views
Not able to replicated Diffbind example dataset.
DiffBind
5 months ago Ayyappa ▴ 10
0
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0
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124
views
Not able to replicated Diffbind example dataset.
DiffBind
5 months ago Ayyappa ▴ 10
0
votes
1
reply
356
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 6 months ago by • 0 • written 7 months ago by • 0
1
vote
1
reply
274
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 6 months ago by ★ 4.4k • written 6 months ago by • 0
3
votes
4
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455
views
dba.contrast in DiffBind
v3.4.0 DiffBind
updated 7 months ago by ★ 4.4k • written 7 months ago by • 0
0
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3
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377
views
DiifBind_DBA_report
DiffBind
updated 7 months ago by ★ 4.4k • written 10 months ago by ▴ 90
3
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4
replies
571
views
DiffBind (Error in if (DBA$config$parallelPackage))
parallel R DiffBind
updated 7 months ago by ★ 4.4k • written 10 months ago by • 0
0
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3
replies
783
views
DiffBind minOverlap parameter
DiffBind minOverlap consensus peakset Job
updated 7 months ago by ★ 4.4k • written 2.7 years ago by • 0
0
votes
1
reply
255
views
diffbind binding affinity matrix
diffbind DiffBind
updated 7 months ago by ★ 4.4k • written 7 months ago by • 0
1
vote
2
replies
345
views
How to include/show/add correction factors/numbers to the Diffbind heat map tiles
DiffBind
updated 7 months ago by ▴ 40 • written 7 months ago by • 0
3
votes
4
replies
1.3k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 8 months ago by ▴ 10 • written 3.9 years ago by ▴ 10
1
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2
replies
315
views
DiffBind in Bioconda
DiffBind Bioconda Versions
9 months ago Riba Michela ▴ 90
0
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0
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218
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
9 months ago Drew • 0
0
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0
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230
views
DiffBind dba.counts memory issue
DiffBind
9 months ago rreese2 • 0
50 results • Page 1 of 1
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Comment: Multi-factorial Time-based design in DEseq2: defining full and reduced model by Alex • 0
Thanks.
Comment: Error message: Could not find function "DESeqDataSetFromMatrix" by James W. MacDonald 60k
Install locfit.
Comment: calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMet by ATpoint ★ 1.3k
Replace `feature_controls` with `subsets`. As said below, type `?calculateQCMetrics` to see the help with avaialble arguments and example c…
Answer: DESeq2 question by Michael Love 37k
This has been posted before on the support site. You can search the site or just click some of the related posts on the right sidebar.
Answer: Multi-factorial Time-based design in DEseq2: defining full and reduced model by Michael Love 37k
For questions about how to formulate particular contrasts in R, I recommend working with a local statistician or someone familiar with line…
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