Showing : diffBind • reset
4
votes
11
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4.6k
views
How to get all possible comparisons in DiffBind
diffbind
updated 3.6 years ago by ★ 5.2k • written 6.7 years ago by ▴ 10
0
votes
7
replies
2.9k
views
dba.count() error when re-centering peaks
DiffBind
updated 3.1 years ago by • 0 • written 3.6 years ago by • 0
0
votes
2
replies
906
views
`dbs.all` object in the vignette
DiffBind
3.6 years ago Mark • 0
1
vote
6
replies
3.7k
views
dba.count error
DiffBind
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by ▴ 10
0
votes
1
reply
703
views
DiffBind issue: zero values for all peaks in one chromosome
DiffBind
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
1
vote
6
replies
2.1k
views
DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
DiffBind dba.count
updated 3.6 years ago by ★ 5.2k • written 3.7 years ago by • 0
2
votes
3
replies
1.2k
views
Not able to replicated Diffbind example dataset.
DiffBind
3.7 years ago Ayyappa ▴ 10
0
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0
replies
723
views
Not able to replicated Diffbind example dataset.
DiffBind
3.7 years ago Ayyappa ▴ 10
1
vote
10
replies
2.2k
views
DiffBind: Values of Called1 and Called2 do not appear to coincide with input peaks
DiffBind
updated 3.6 years ago by ★ 5.2k • written 3.7 years ago by • 0
1
vote
1
reply
1.5k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
6
votes
19
replies
8.5k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 2.1 years ago by • 0 • written 4.1 years ago by ▴ 10
2
votes
4
replies
2.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 19 months ago by ▴ 10 • written 3.8 years ago by • 0
0
votes
1
reply
1.1k
views
diffbind binding affinity matrix
diffbind DiffBind
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
0
votes
2
replies
3.0k
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 3.2 years ago by ▴ 10 • written 3.8 years ago by • 0
3
votes
4
replies
4.0k
views
dba.contrast in DiffBind
v3.4.0 DiffBind
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
1
vote
2
replies
1.2k
views
How to include/show/add correction factors/numbers to the Diffbind heat map tiles
DiffBind
updated 3.8 years ago by ▴ 60 • written 3.8 years ago by • 0
3
votes
4
replies
3.2k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 3.9 years ago by ▴ 10 • written 7.1 years ago by ▴ 10
0
votes
0
replies
1.3k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.9 years ago Drew • 0
1
vote
2
replies
1.6k
views
DiffBind in Bioconda
DiffBind Bioconda Versions
4.0 years ago • updated 3.9 years ago Riba Michela ▴ 90
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0
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1.2k
views
DiffBind dba.counts memory issue
DiffBind
4.0 years ago rreese2 • 0
0
votes
2
replies
2.1k
views
how to select specific genes from heatmap of differentially accessible regions of ATAC-seq in DiffBind
DiffBind
updated 4.0 years ago by ★ 5.2k • written 4.0 years ago by • 0
0
votes
1
reply
1.2k
views
Can DiffBind do differential analysis for un-paired peaksets?
DiffBind
updated 4.0 years ago by ★ 5.2k • written 4.0 years ago by • 0
0
votes
2
replies
1.8k
views
Diffbind dba.plotProfile attempt to select less than one element in OneIndex
DiffBind
4.0 years ago bhanratt • 0
0
votes
3
replies
1.1k
views
DiifBind_DBA_report
DiffBind
updated 3.8 years ago by ★ 5.2k • written 4.0 years ago by ▴ 90
2
votes
1
reply
1.4k
views
Diffbind: differences between design vs no design (same comparison)?
DiffBind
updated 4.0 years ago by ★ 5.2k • written 4.0 years ago by • 0
1
vote
2
replies
1.2k
views
DiffBind fold parameter vs. IfcThreshold in DESeq2
DiffBind
4.0 years ago Shuwan ▴ 10
3
votes
4
replies
2.0k
views
DiffBind (Error in if (DBA$config$parallelPackage))
parallel R DiffBind
updated 3.8 years ago by ★ 5.2k • written 4.1 years ago by • 0
0
votes
3
replies
1.1k
views
DiffBind Occupancy analysis
DiffBind
updated 4.1 years ago by ★ 5.2k • written 4.1 years ago by • 0
1
vote
3
replies
1.8k
views
issue with DiffBind dba.count
bam bai DiffBind dba.count Diffbind
updated 4.1 years ago by ★ 5.2k • written 4.1 years ago by ▴ 10
0
votes
0
replies
790
views
Diffbind issue
DiffBind
4.1 years ago mtsompana ▴ 10
3
votes
12
replies
5.0k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.1 years ago by ★ 5.2k • written 6.0 years ago by ▴ 20
0
votes
0
replies
847
views
DiffBind error during normalization
DiffBind
4.1 years ago jseg ▴ 10
0
votes
2
replies
1.5k
views
DiffBind
bflip dba.report DiffBind
4.1 years ago • updated 4.0 years ago Riba Michela ▴ 90
2
votes
3
replies
2.2k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.0 years ago by ▴ 20 • written 4.1 years ago by • 0
1
vote
3
replies
2.3k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 4.1 years ago by ▴ 80 • written 4.1 years ago by • 0
0
votes
0
replies
803
views
Diffbind without replicates
DiffBind
4.2 years ago Danielle • 0
5
votes
8
replies
3.2k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.3 years ago by ▴ 20 • written 4.2 years ago by ▴ 30
1
vote
1
reply
1.5k
views
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
DESeq2 Diffbind
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by ▴ 10
1
vote
2
replies
1.0k
views
Output of normalizing a dba object with DBA_DESEQ2,normalize = DBA_NORM_RLE in Diffbind
DiffBind
4.2 years ago Alexandre ▴ 10
0
votes
0
replies
1.1k
views
Are broad/narrow peak comparable?
Peaks MAC2 DiffBind
4.2 years ago Yuan Tian ▴ 290
0
votes
0
replies
756
views
Interpretation of diffbind coefficients
DiffBind
4.2 years ago Alexandre ▴ 10
1
vote
2
replies
1.1k
views
DiffBind dba.report(): Question about DBA_ALL_METHODS
DiffBind
4.2 years ago etiennedanis • 0
1
vote
1
reply
864
views
How are greylists derived in DiffBind
DiffBind
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by ▴ 10
2
votes
1
reply
5.9k
views
DiffBind Error in if (file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed
DiffBind
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by ▴ 10
1
vote
1
reply
1.2k
views
DiffBind normalisation factor retrieval
edgeR Normalization DiffBind
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by • 0
12
votes
6
replies
6.4k
views
How to select summit size for histone ChiP-Seq in Diffbind
Diffbind Histone Chip-Seq Summit size
updated 3.3 years ago by ★ 5.2k • written 8.0 years ago by ▴ 40
1
vote
4
replies
2.2k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
4.2 years ago sh.kazempour94 ▴ 10
0
votes
1
reply
1.0k
views
Hard coding in DiffBind DBA.R line 968
DiffBind
updated 4.3 years ago by ★ 5.2k • written 4.3 years ago by ★ 1.3k
0
votes
1
reply
1.1k
views
DiffBind confusions
DiffBind
updated 4.3 years ago by ★ 5.2k • written 4.3 years ago by • 0
2
votes
8
replies
2.9k
views
DiffBind -- Error: No sites have activity greater than minMaxval
DiffBind
updated 3.0 years ago by • 0 • written 4.3 years ago by ▴ 10
678 results • Page 4 of 14
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
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Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
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There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
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What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
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