Showing : DiffBind • reset
0
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3
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107
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
updated 9 hours ago by ★ 4.0k • written 2 days ago by • 0
0
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0
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59
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
3 days ago Virangika • 0
2
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2
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135
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[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 3 days ago Henry ▴ 10
2
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2
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336
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
7 days ago Henry ▴ 10
0
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0
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92
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
21 days ago feather-W • 0
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0
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91
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
21 days ago Ankit ▴ 20
0
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0
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78
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
22 days ago Pierre Lindenbaum ▴ 10
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0
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119
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
29 days ago erbrocato • 0
0
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2
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218
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
5 weeks ago Sam ▴ 10
0
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1
reply
178
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Exact same results in Diffbind with different normalization methods
DiffBind
5 weeks ago • updated 4 weeks ago red_bricks ▴ 50
0
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1
reply
279
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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
0
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0
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220
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 weeks ago Jawahar • 0
0
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0
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161
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
0
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0
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150
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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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212
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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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234
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
0
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1
reply
905
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by • 0 • written 7 months ago by • 0
0
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2
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327
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
vote
2
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312
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
vote
1
reply
332
views
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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315
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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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382
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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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
replies
448
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 0
1
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1
reply
425
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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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831
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
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3
replies
603
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
525
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
replies
589
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
votes
2
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443
views
DiffBind error
DiffBind
updated 7 months ago by ★ 5.1k • written 8 months ago by • 0
0
votes
2
replies
785
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 8 months ago by ★ 1.6k • written 8 months ago by • 0
1
vote
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
votes
5
replies
2.9k
views
diffbind
DiffBind chipseq
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
0
votes
3
replies
601
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
votes
5
replies
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
vote
4
replies
810
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
659
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
528
views
DiffBind output issues
DiffBind
updated 9 months ago by ★ 5.1k • written 10 months ago by • 0
1
vote
2
replies
743
views
Interpret plots from DiffBind
DiffBind
10 months ago • updated 9 months ago Chris • 0
2
votes
3
replies
591
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
votes
4
replies
785
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago • updated 9 months ago bhandary.8590 ▴ 20
0
votes
0
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412
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 4 months ago by 65k • written 10 months ago by • 0
7
votes
13
replies
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
replies
393
views
Title in dba.plotProfile
DiffBind
10 months ago agata17 • 0
0
votes
1
reply
546
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
638
views
DiffBind dba() in parallel
DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
1
vote
4
replies
987
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
1
vote
0
replies
543
views
Fold values in Diffbind
DiffBind
11 months ago bhandary.8590 ▴ 20
50 results • Page 1 of 1
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Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
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Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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