Showing : diffBind • reset
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44
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dba.plotProfile() plotting and interpretation
DiffBind
1 day ago Henry ▴ 10
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41
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
3 days ago yvonneh • 0
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37
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
3 days ago Ian D. ▴ 70
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2
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118
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
4 days ago • updated 3 days ago Ian D. ▴ 70
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101
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
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1
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131
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ATACseq merge peaks
DiffBind
updated 9 days ago by ★ 4.1k • written 10 days ago by • 0
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4
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235
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
18 days ago • updated 15 days ago lonn • 0
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94
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
19 days ago Virangika • 0
2
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2
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171
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[DiffBind] Obtaining normalization factors
DiffBind
23 days ago • updated 19 days ago Henry ▴ 10
2
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2
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387
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
23 days ago Henry ▴ 10
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0
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111
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
5 weeks ago feather-W • 0
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110
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
5 weeks ago Ankit ▴ 20
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98
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
5 weeks ago Pierre Lindenbaum ▴ 10
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0
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140
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
6 weeks ago erbrocato • 0
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2
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248
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
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1
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199
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Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago red_bricks ▴ 50
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1
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299
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
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245
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
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176
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
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0
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169
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Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
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0
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242
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
4 months ago Hai • 0
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0
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259
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
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1
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936
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DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by • 0 • written 8 months ago by • 0
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2
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353
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
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2
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330
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Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
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1
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356
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
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333
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
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410
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 7 months ago by 65k • written 7 months ago by • 0
2
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4
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1.2k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 6 months ago by • 0 • written 7 months ago by • 0
2
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2
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467
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DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 0
1
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1
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452
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DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 7 months ago by 65k • written 7 months ago by • 0
3
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7
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863
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
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3
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633
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diffbind analyze for wheat
DiffBind
updated 9 weeks ago by • 0 • written 7 months ago by • 0
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1
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546
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Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago Mark • 0
1
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2
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629
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DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
0
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2
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488
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DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
0
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2
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838
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
1
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1
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1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
1
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1
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2.3k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 9 months ago by ▴ 20
0
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5
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3.1k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
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3
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634
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DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
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5
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1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by ★ 5.2k • written 4.2 years ago by • 0
1
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4
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875
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
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683
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DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
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1
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549
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
1
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2
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779
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Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
2
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3
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615
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Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
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4
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817
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DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
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0
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430
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
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7
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1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
50 results • Page 1 of 1
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Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
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I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
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The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
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It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
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These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
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