Showing : DiFFBind • reset
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21
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
17 hours ago • updated 16 hours ago yvonneh • 0
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0
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19
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
17 hours ago Ian D. ▴ 70
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2
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92
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 17 hours ago Ian D. ▴ 70
1
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1
reply
84
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
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1
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117
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ATACseq merge peaks
DiffBind
updated 6 days ago by ★ 4.1k • written 8 days ago by • 0
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4
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230
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 days ago • updated 13 days ago lonn • 0
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0
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93
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
17 days ago Virangika • 0
2
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2
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166
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[DiffBind] Obtaining normalization factors
DiffBind
20 days ago • updated 16 days ago Henry ▴ 10
2
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2
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379
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
21 days ago • updated 20 days ago Henry ▴ 10
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0
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109
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
4 weeks ago feather-W • 0
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0
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109
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
4 weeks ago Ankit ▴ 20
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93
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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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139
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
6 weeks ago erbrocato • 0
0
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2
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243
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
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1
reply
195
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Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago red_bricks ▴ 50
0
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1
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298
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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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0
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244
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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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0
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175
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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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168
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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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237
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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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256
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
1
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2
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326
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
0
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2
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349
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
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1
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354
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
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0
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332
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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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0
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406
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 6 months ago by 65k • written 6 months ago by • 0
2
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2
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463
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DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago • updated 6 months ago r.murakami • 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
1
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1
reply
448
views
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
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3
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631
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diffbind analyze for wheat
DiffBind
updated 9 weeks ago by • 0 • written 7 months ago by • 0
3
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7
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859
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
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1
reply
543
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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
0
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1
reply
931
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by • 0 • written 8 months ago by • 0
0
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2
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481
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
1
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2
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617
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
0
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3
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627
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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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2
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833
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
0
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5
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3.0k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
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1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 9 months ago by ▴ 20
1
vote
4
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867
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
678
views
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
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
2
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3
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609
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
votes
4
replies
811
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
1
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2
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772
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
0
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1
reply
544
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
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0
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428
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
0
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0
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410
views
Title in dba.plotProfile
DiffBind
11 months ago agata17 • 0
8
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13
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1.9k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
50 results • Page 1 of 1
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Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
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Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
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Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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