Showing : diffbind • reset
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23
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
1 day ago Dinesh • 0
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68
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dba.plotProfile() plotting and interpretation
DiffBind
4 days ago Henry ▴ 10
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51
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
5 days ago yvonneh • 0
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46
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
5 days ago Ian D. ▴ 70
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2
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139
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
6 days ago • updated 5 days ago Ian D. ▴ 70
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116
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
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1
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140
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ATACseq merge peaks
DiffBind
updated 11 days ago by ★ 4.1k • written 13 days ago by • 0
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4
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241
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
20 days ago • updated 17 days ago lonn • 0
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96
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
22 days ago Virangika • 0
2
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2
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172
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[DiffBind] Obtaining normalization factors
DiffBind
25 days ago • updated 21 days ago Henry ▴ 10
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2
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392
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
26 days ago • updated 25 days ago Henry ▴ 10
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115
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
5 weeks ago feather-W • 0
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112
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
5 weeks ago Ankit ▴ 20
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100
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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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142
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
6 weeks ago erbrocato • 0
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2
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253
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 weeks ago • updated 7 weeks ago Sam ▴ 10
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1
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200
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Exact same results in Diffbind with different normalization methods
DiffBind
8 weeks ago • updated 7 weeks ago red_bricks ▴ 50
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1
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303
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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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247
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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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178
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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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172
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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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244
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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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261
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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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941
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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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356
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
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2
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331
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Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
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1
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360
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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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334
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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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412
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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
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4
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1.2k
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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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470
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DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 0
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456
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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
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867
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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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638
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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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552
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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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633
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DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago Junsik • 0
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2
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491
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DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
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2
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846
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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
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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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638
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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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1.2k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by ★ 5.2k • written 4.3 years ago by • 0
1
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4
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879
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diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
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2
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689
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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
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1
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550
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DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
1
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2
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783
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Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
2
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3
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621
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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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826
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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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436
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Help with error running DiffBind
DiffBind
11 months ago Chris • 0
50 results • Page 1 of 1
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Replies
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(fit2, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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