Showing : Diffbind • reset
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DiffBind
bflip dba.report DiffBind
updated 1 day ago by ★ 4.0k • written 2 days ago by ▴ 80
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2
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132
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An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
5 days ago • updated 2 days ago zhuyi05 • 0
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36
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DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
5 days ago kwangbom • 0
1
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3
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89
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Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 8 days ago by ▴ 70 • written 10 days ago by • 0
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47
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Diffbind without replicates
DiffBind
11 days ago Danielle • 0
5
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7
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246
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
15 days ago • updated 11 days ago pegah.taklifi ▴ 30
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1
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70
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DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
DESeq2 Diffbind
updated 12 days ago by ★ 4.0k • written 19 days ago by • 0
1
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2
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98
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Output of normalizing a dba object with DBA_DESEQ2,normalize = DBA_NORM_RLE in Diffbind
DiffBind
22 days ago • updated 11 days ago Alexandre • 0
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49
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Are broad/narrow peak comparable?
Peaks MAC2 DiffBind
13 days ago Yuan Tian ▴ 240
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49
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Interpretation of diffbind coefficients
DiffBind
19 days ago Alexandre • 0
1
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2
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108
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DiffBind dba.report(): Question about DBA_ALL_METHODS
DiffBind
25 days ago • updated 15 days ago etiennedanis • 0
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1
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71
views
How are greylists derived in DiffBind
DiffBind
updated 4 weeks ago by ★ 4.0k • written 4 weeks ago by • 0
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1
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92
views
DiffBind Error in if (file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed
DiffBind
updated 4 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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1
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99
views
DiffBind normalisation factor retrieval
edgeR Normalization DiffBind
updated 4 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
8
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4
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1.6k
views
How to select summit size for histone ChiP-Seq in Diffbind
Diffbind Histone Chip-Seq Summit size
updated 6 weeks ago by ★ 4.0k • written 3.9 years ago by ▴ 40
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4
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215
views
Binding matrix created by DiffBind
ATACSeq DiffBind
6 weeks ago • updated 5 weeks ago sh.kazempour94 ▴ 10
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1
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129
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Hard coding in DiffBind DBA.R line 968
DiffBind
updated 7 weeks ago by ★ 4.0k • written 7 weeks ago by ★ 1.2k
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1
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262
views
DiffBind confusions
DiffBind
updated 7 weeks ago by ★ 4.0k • written 7 weeks ago by • 0
2
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7
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249
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DiffBind -- Error: No sites have activity greater than minMaxval
DiffBind
updated 24 days ago by ★ 4.0k • written 7 weeks ago by • 0
0
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1
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127
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 9 weeks ago by 57k • written 9 weeks ago by ▴ 240
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144
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
9 weeks ago Rory Stark ★ 4.0k
2
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5
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217
views
erorr in normalization with DiffBind: pv$binding[, colnum] <- pv$peaks[[i]]$RPKM: number of items to replace is not a multiple of replacement length
DiffBind
10 weeks ago ben.vanderveer • 0
2
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3
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190
views
Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind dba.plotPCA
updated 11 weeks ago by ★ 4.0k • written 11 weeks ago by • 0
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4
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960
views
DiffBind not accessible files in Example data
diffbind
updated 11 weeks ago by ★ 4.0k • written 3.6 years ago by • 0
0
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4
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265
views
DiffBind
ATACSeq DiFFBind
3 months ago • updated 10 weeks ago Riba Michela ▴ 80
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110
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DiffBind reporting error
DiffBind
11 weeks ago Ivan • 0
1
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2
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719
views
diffBind report Fold scale
diffBind Fold Change
updated 12 weeks ago by • 0 • written 2.5 years ago by • 0
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4
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370
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 12 weeks ago by ★ 4.0k • written 22 months ago by ▴ 20
2
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1
reply
177
views
How to retrieve peak summit from DiffBind peaks
DiffBind
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
1
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2
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316
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
3 months ago mwong043 • 0
2
votes
1
reply
145
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 3 months ago by ★ 4.0k • written 3 months ago by ▴ 10
2
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2
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243
views
A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 3 months ago by ★ 4.0k • written 4 months ago by ▴ 10
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7
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289
views
DiffBind DEseq
DiffBind
3 months ago 浩然 • 0
0
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138
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
4 months ago Goku • 0
2
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6
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278
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
4 months ago Goku • 0
4
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7
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419
views
DiffBind how to retrieve normalized count matrix of ATAC-seq data
DiffBind
updated 3 months ago by ★ 4.0k • written 4 months ago by ▴ 10
1
vote
1
reply
186
views
diffbind installation through Conda fails
DiffBind conda
updated 4 months ago by ★ 4.0k • written 4 months ago by ▴ 90
1
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5
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289
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 4 months ago by 57k • written 4 months ago by • 0
0
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4
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336
views
How sensitive is DiffBind to Deseq2 assumptions ?
DESeq2 DiffBind
updated 3 months ago by ★ 4.0k • written 4 months ago by ▴ 10
1
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3
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218
views
DiffBind: bGain or bLoss parameters in dba.report don't work?
DiffBind
4 months ago fleur_p90 • 0
1
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4
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282
views
DiffBind: dba.contrast for interaction terms
DiffBind
updated 3 months ago by ★ 4.0k • written 4 months ago by • 0
0
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1
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142
views
DiffBind with spike in
DiffBind
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
1
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2
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218
views
Diffbind error while running example data
DiffBind
5 months ago • updated 4 months ago Lucky • 0
1
vote
1
reply
156
views
DiffBind fragmentSize meaning
DiffBind
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
2
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4
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252
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
1
vote
1
reply
159
views
Diffbind principal components
PCA DiffBind
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
1
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4
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252
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
5 months ago • updated 4 months ago SFn • 0
1
vote
14
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513
views
error: DBA object is already formed from a consensus peakset
DiffBind
6 months ago • updated 5 months ago ahua217 ▴ 10
2
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2
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354
views
DiffBind installation fails: Error: package ‘BiocGenerics’ 0.34.0 is loaded, but >= 0.36.0 is required by ‘IRanges’
systemPipeR Bioconductor DiffBind BiocGenerics
updated 6 months ago by 25k • written 6 months ago by • 0
1
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1
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175
views
dba.count() of DiffBind 3.0 does not have bSubControl parameter
DiffBind
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: featureCounts - paired-end data by Yanfang • 0
Hey Wei shi, May I ask you something related to featureCounts? I have only paired end reads (RNAseq) mapping to its genome by bowtie2, an…
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Cross-posted: https://www.biostars.org/p/9482927/
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Hi @maltethodberg We currently do not have a method that does this. Perhaps a `duplicated` method is appropriate but I am not the develop…
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Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
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I should note that when I query org.Mm.eg.db using the gene Symbols associated with my differential expression data I find a 1:1 correspond…
Votes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
A: Normalized counts of DESeq2 affected by design formula?
A: Finding orthologous human/mouse ENSEMBL IDs
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Answer: What lfcSE is dependent upon?
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