Showing : diffBind • reset
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15
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
14 hours ago lonn • 0
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0
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45
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
2 days ago Virangika • 0
2
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2
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123
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[DiffBind] Obtaining normalization factors
DiffBind
5 days ago • updated 1 day ago Henry ▴ 10
2
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2
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331
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
6 days ago • updated 5 days ago Henry ▴ 10
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0
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91
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
19 days ago feather-W • 0
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85
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
19 days ago Ankit ▴ 20
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76
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
20 days ago Pierre Lindenbaum ▴ 10
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116
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
28 days ago erbrocato • 0
0
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2
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215
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
5 weeks ago • updated 4 weeks ago Sam ▴ 10
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1
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174
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Exact same results in Diffbind with different normalization methods
DiffBind
5 weeks ago • updated 4 weeks ago red_bricks ▴ 50
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1
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276
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
12 weeks ago isaromero8888 • 0
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0
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218
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 weeks ago Jawahar • 0
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157
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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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147
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Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
0
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0
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210
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
3 months ago Hai • 0
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0
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231
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
0
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1
reply
904
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DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by • 0 • written 7 months ago by • 0
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2
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321
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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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307
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Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
vote
1
reply
331
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
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0
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311
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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
0
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0
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379
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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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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 6 months ago by • 0
2
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2
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446
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DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 0
1
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1
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423
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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 6 months ago by 65k • written 6 months ago by • 0
3
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7
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828
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
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3
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597
views
diffbind analyze for wheat
DiffBind
updated 7 weeks ago by • 0 • written 7 months ago by • 0
0
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1
reply
520
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
7 months ago Mark • 0
1
vote
2
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585
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago • updated 7 months ago Junsik • 0
0
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2
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440
views
DiffBind error
DiffBind
updated 7 months ago by ★ 5.1k • written 8 months ago by • 0
0
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2
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782
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 8 months ago by ★ 1.6k • written 8 months ago by • 0
1
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1
reply
1.8k
views
Help with error DiffBind
DiffBind
updated 8 months ago by ★ 5.1k • written 9 months ago by • 0
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 8 months ago by ★ 5.1k • written 9 months ago by ▴ 20
0
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5
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2.9k
views
diffbind
DiffBind chipseq
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
0
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3
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596
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 8 months ago by ★ 5.1k • written 8 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 6 months ago by ★ 5.1k • written 4.2 years ago by • 0
1
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4
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808
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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655
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
0
votes
1
reply
527
views
DiffBind output issues
DiffBind
updated 9 months ago by ★ 5.1k • written 10 months ago by • 0
1
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2
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739
views
Interpret plots from DiffBind
DiffBind
10 months ago • updated 9 months ago Chris • 0
2
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3
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588
views
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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783
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago • updated 9 months ago bhandary.8590 ▴ 20
0
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0
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409
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
vote
7
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1.2k
views
Diffbind "No genome detected"
DiffBind
updated 4 months ago by 65k • written 10 months ago by • 0
7
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13
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1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.1k • written 10 months ago by • 0
0
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0
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391
views
Title in dba.plotProfile
DiffBind
10 months ago agata17 • 0
0
votes
1
reply
545
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 10 months ago by ★ 5.1k • written 11 months ago by ▴ 10
0
votes
1
reply
635
views
DiffBind dba() in parallel
DiffBind
updated 10 months ago by ★ 5.1k • written 10 months ago by • 0
1
vote
4
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980
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.1k • written 10 months ago by • 0
1
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0
replies
542
views
Fold values in Diffbind
DiffBind
10 months ago bhandary.8590 ▴ 20
50 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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