Showing : diffBind • reset
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how to select specific genes from heatmap of differentially accessible regions of ATAC-seq in DiffBind
DiffBind
18 hours ago Laura • 0
0
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1
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82
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Can DiffBind do differential analysis for un-paired peaksets?
DiffBind
updated 3 days ago by ★ 4.1k • written 6 days ago by • 0
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1
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113
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Diffbind dba.plotProfile attempt to select less than one element in OneIndex
DiffBind
updated 3 days ago by ★ 4.1k • written 4 days ago by • 0
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1
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86
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DiifBind_DBA_report
DiffBind
updated 8 days ago by ★ 4.1k • written 9 days ago by ▴ 80
2
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1
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116
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Diffbind: differences between design vs no design (same comparison)?
DiffBind
updated 11 days ago by ★ 4.1k • written 15 days ago by • 0
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2
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103
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DiffBind fold parameter vs. IfcThreshold in DESeq2
DiffBind
16 days ago • updated 14 days ago Shuwan ▴ 10
2
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2
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75
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DiffBind (Error in if (DBA$config$parallelPackage))
parallel R DiffBind
23 days ago • updated 22 days ago eggrandio • 0
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3
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91
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DiffBind Occupancy analysis
DiffBind
updated 22 days ago by ★ 4.1k • written 4 weeks ago by • 0
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3
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146
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issue with DiffBind dba.count
bam bai DiffBind dba.count Diffbind
updated 22 days ago by ★ 4.1k • written 5 weeks ago by • 0
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0
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42
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Diffbind issue
DiffBind
5 weeks ago mtsompana • 0
3
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12
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608
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 5 weeks ago by ★ 4.1k • written 2.0 years ago by ▴ 20
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2
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170
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DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 21 days ago by ▴ 20 • written 7 weeks ago by • 0
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0
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78
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DiffBind error during normalization
DiffBind
6 weeks ago jseg • 0
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2
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131
views
DiffBind
bflip dba.report DiffBind
7 weeks ago • updated 20 days ago Riba Michela ▴ 80
2
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3
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231
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An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 14 days ago by ▴ 20 • written 7 weeks ago by • 0
1
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3
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159
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Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 7 weeks ago by ▴ 70 • written 8 weeks ago by • 0
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89
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Diffbind without replicates
DiffBind
8 weeks ago Danielle • 0
5
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7
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324
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
8 weeks ago pegah.taklifi ▴ 30
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1
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116
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DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
DESeq2 Diffbind
updated 8 weeks ago by ★ 4.1k • written 9 weeks ago by • 0
1
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2
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142
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Output of normalizing a dba object with DBA_DESEQ2,normalize = DBA_NORM_RLE in Diffbind
DiffBind
9 weeks ago • updated 8 weeks ago Alexandre • 0
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93
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Are broad/narrow peak comparable?
Peaks MAC2 DiffBind
8 weeks ago Yuan Tian ▴ 240
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84
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Interpretation of diffbind coefficients
DiffBind
9 weeks ago Alexandre • 0
1
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2
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148
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DiffBind dba.report(): Question about DBA_ALL_METHODS
DiffBind
10 weeks ago • updated 8 weeks ago etiennedanis • 0
1
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1
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103
views
How are greylists derived in DiffBind
DiffBind
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
2
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1
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128
views
DiffBind Error in if (file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed
DiffBind
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
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1
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133
views
DiffBind normalisation factor retrieval
edgeR Normalization DiffBind
updated 11 weeks ago by ★ 4.1k • written 3 months ago by • 0
9
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4
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1.8k
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How to select summit size for histone ChiP-Seq in Diffbind
Diffbind Histone Chip-Seq Summit size
updated 3 months ago by ★ 4.1k • written 4.0 years ago by ▴ 40
1
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4
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273
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3 months ago • updated 12 weeks ago sh.kazempour94 ▴ 10
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159
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Hard coding in DiffBind DBA.R line 968
DiffBind
updated 3 months ago by ★ 4.1k • written 3 months ago by ★ 1.2k
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1
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292
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DiffBind confusions
DiffBind
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
2
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7
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305
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DiffBind -- Error: No sites have activity greater than minMaxval
DiffBind
updated 10 weeks ago by ★ 4.1k • written 3 months ago by • 0
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1
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212
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DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3 months ago by 58k • written 3 months ago by ▴ 240
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2
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293
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
3 months ago • updated 13 days ago Rory Stark ★ 4.1k
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5
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269
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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
4 months ago ben.vanderveer • 0
2
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3
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238
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Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind dba.plotPCA
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
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4
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1.0k
views
DiffBind not accessible files in Example data
diffbind
updated 4 months ago by ★ 4.1k • written 3.8 years ago by • 0
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4
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314
views
DiffBind
ATACSeq DiFFBind
4 months ago Riba Michela ▴ 80
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0
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145
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DiffBind reporting error
DiffBind
4 months ago Ivan • 0
1
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2
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801
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diffBind report Fold scale
diffBind Fold Change
updated 4 months ago by • 0 • written 2.7 years ago by • 0
2
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1
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245
views
How to retrieve peak summit from DiffBind peaks
DiffBind
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
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3
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419
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CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
updated 6 weeks ago by ★ 4.1k • written 5 months ago by • 0
2
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1
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175
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 5 months ago by ★ 4.1k • written 5 months ago by ▴ 10
2
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2
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288
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A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 5 months ago by ★ 4.1k • written 5 months ago by ▴ 10
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7
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337
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DiffBind DEseq
DiffBind
5 months ago 浩然 • 0
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0
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201
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
5 months ago Goku • 0
2
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6
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320
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
5 months ago Goku • 0
4
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7
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529
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DiffBind how to retrieve normalized count matrix of ATAC-seq data
DiffBind
updated 5 months ago by ★ 4.1k • written 5 months ago by ▴ 10
1
vote
1
reply
231
views
diffbind installation through Conda fails
DiffBind conda
updated 5 months ago by ★ 4.1k • written 5 months ago by ▴ 90
1
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5
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339
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 5 months ago by 58k • written 6 months ago by • 0
0
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4
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381
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How sensitive is DiffBind to Deseq2 assumptions ?
DESeq2 DiffBind
updated 5 months ago by ★ 4.1k • written 6 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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