Showing : diffBind • reset
2
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4
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99
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Diffbind dba$binding slot finding Chr21 for an MM10 dataset
DiffBind
updated 3 days ago by ★ 4.4k • written 4 days ago by • 0
0
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3
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80
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DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3 days ago by ★ 4.4k • written 4 days ago by • 0
0
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2
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94
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DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
updated 3 days ago by ★ 4.4k • written 24 days ago by • 0
0
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1
reply
143
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 5 weeks ago by ★ 4.4k • written 9 weeks ago by • 0
0
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0
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72
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DiffBind does not load samples
DiffBind
5 weeks ago nw416 • 0
3
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5
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596
views
Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind dba.plotPCA
updated 5 weeks ago by ★ 4.4k • written 12 months ago by ▴ 10
1
vote
1
reply
151
views
DiffBind drop out some peaks
DiffBind
updated 5 weeks ago by ★ 4.4k • written 6 weeks ago by • 0
0
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0
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62
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Creating a consensus peakset in DiffBind for all the conditions of an experiment
DiffBind
5 weeks ago Sam ▴ 10
1
vote
2
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201
views
BiocParallel error when running DiffBind
BiocParallel BiocPa DiffBind
updated 6 weeks ago by 25k • written 10 weeks ago by ▴ 10
0
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0
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80
views
DiffBind error
DiffBind DifferentialPeakCalling
9 weeks ago Amandeep • 0
0
votes
1
reply
134
views
DiffBind contrast design - pairwise with independent filtering
DiffBind
updated 6 days ago by • 0 • written 9 weeks ago by • 0
0
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9
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952
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Questions about DiffBind loaded peaks and re-count reads
DiffBind
17 months ago • updated 12 weeks ago Tongjun • 0
5
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6
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306
views
How to get 3/4 peak overlap in DiffBind?
DiffBind
3 months ago • updated 12 weeks ago Krista • 0
3
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11
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1.4k
views
How to get all possible comparisons in DiffBind
diffbind
updated 3 months ago by ★ 4.4k • written 3.4 years ago by • 0
0
votes
2
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301
views
dba.count() error when re-centering peaks
DiffBind
3 months ago Mark • 0
0
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2
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182
views
`dbs.all` object in the vignette
DiffBind
3 months ago Mark • 0
1
vote
6
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506
views
dba.count error
DiffBind
updated 3 months ago by ★ 4.4k • written 3 months ago by ▴ 10
0
votes
1
reply
106
views
DiffBind issue: zero values for all peaks in one chromosome
DiffBind
updated 3 months ago by ★ 4.4k • written 3 months ago by • 0
1
vote
6
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431
views
DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
DiffBind dba.count
updated 3 months ago by ★ 4.4k • written 4 months ago by • 0
2
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3
replies
242
views
Not able to replicated Diffbind example dataset.
DiffBind
4 months ago • updated 3 months ago Ayyappa ▴ 10
0
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0
replies
102
views
Not able to replicated Diffbind example dataset.
DiffBind
4 months ago Ayyappa ▴ 10
1
vote
10
replies
525
views
DiffBind: Values of Called1 and Called2 do not appear to coincide with input peaks
DiffBind
updated 3 months ago by ★ 4.4k • written 4 months ago by • 0
1
vote
1
reply
238
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 4 months ago by ★ 4.4k • written 5 months ago by • 0
0
votes
5
replies
892
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 1 hour ago by ★ 4.4k • written 9 months ago by • 0
0
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1
reply
289
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 4 months ago by • 0 • written 5 months ago by • 0
0
votes
1
reply
227
views
diffbind binding affinity matrix
diffbind DiffBind
updated 5 months ago by ★ 4.4k • written 6 months ago by • 0
0
votes
1
reply
758
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 5 months ago by ★ 4.4k • written 5 months ago by • 0
3
votes
4
replies
355
views
dba.contrast in DiffBind
v3.4.0 DiffBind
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
1
vote
2
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316
views
How to include/show/add correction factors/numbers to the Diffbind heat map tiles
DiffBind
updated 6 months ago by ▴ 40 • written 6 months ago by • 0
3
votes
4
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1.2k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 7 months ago by ▴ 10 • written 3.8 years ago by ▴ 10
0
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0
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179
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
7 months ago Drew • 0
1
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2
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273
views
DiffBind in Bioconda
DiffBind Bioconda Versions
7 months ago Riba Michela ▴ 90
0
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0
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190
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DiffBind dba.counts memory issue
DiffBind
7 months ago rreese2 • 0
0
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2
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300
views
how to select specific genes from heatmap of differentially accessible regions of ATAC-seq in DiffBind
DiffBind
updated 7 months ago by ★ 4.4k • written 8 months ago by • 0
0
votes
1
reply
236
views
Can DiffBind do differential analysis for un-paired peaksets?
DiffBind
updated 8 months ago by ★ 4.4k • written 8 months ago by • 0
0
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2
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485
views
Diffbind dba.plotProfile attempt to select less than one element in OneIndex
DiffBind
8 months ago bhanratt • 0
0
votes
3
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341
views
DiifBind_DBA_report
DiffBind
updated 5 months ago by ★ 4.4k • written 8 months ago by ▴ 90
2
votes
1
reply
299
views
Diffbind: differences between design vs no design (same comparison)?
DiffBind
updated 8 months ago by ★ 4.4k • written 8 months ago by • 0
1
vote
2
replies
267
views
DiffBind fold parameter vs. IfcThreshold in DESeq2
DiffBind
8 months ago Shuwan ▴ 10
3
votes
4
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531
views
DiffBind (Error in if (DBA$config$parallelPackage))
parallel R DiffBind
updated 5 months ago by ★ 4.4k • written 8 months ago by • 0
0
votes
3
replies
243
views
DiffBind Occupancy analysis
DiffBind
updated 8 months ago by ★ 4.4k • written 9 months ago by • 0
1
vote
3
replies
388
views
issue with DiffBind dba.count
bam bai DiffBind dba.count Diffbind
updated 8 months ago by ★ 4.4k • written 9 months ago by ▴ 10
0
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0
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156
views
Diffbind issue
DiffBind
9 months ago mtsompana ▴ 10
3
votes
12
replies
1.0k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 9 months ago by ★ 4.4k • written 2.7 years ago by ▴ 20
0
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0
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216
views
DiffBind error during normalization
DiffBind
9 months ago jseg ▴ 10
0
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2
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269
views
DiffBind
bflip dba.report DiffBind
9 months ago • updated 8 months ago Riba Michela ▴ 90
2
votes
3
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414
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 8 months ago by ▴ 20 • written 9 months ago by • 0
1
vote
3
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387
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 9 months ago by ▴ 70 • written 9 months ago by • 0
0
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0
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187
views
Diffbind without replicates
DiffBind
9 months ago Danielle • 0
5
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7
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647
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 6 weeks ago by • 0 • written 10 months ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Comment: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by Yang Shi • 0
Perfect answer! This questions troubled me for a long time. Thanks again and for your quick and detailed reply.
Comment: HTSeq Counts no longer available by swbarnes2 ★ 1.0k
STAR's output was intended to mimic HTseq-counts.
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by James W. MacDonald 59k
In the previous post I noted that `paCalls` doesn't exist for this array, and that is still true today. And there are no methods similar to…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by Rory Stark ★ 4.4k
Could you let me know the versions? Output of `sessionInfo()`.
Comment: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o by Yang Shi • 0
okay sir, the new post is here (https://support.bioconductor.org/p/9144266/). Looking forward to your reply.
Votes
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
Comment: Problem converting transcript to genomic coordinates with Annotation Hub
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
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Popular Question to Johannes Rainer ★ 1.9k
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