Showing : DiffBind • reset
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56
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ATACseq merge peaks
DiffBind
updated 18 hours ago by ★ 4.0k • written 2 days ago by • 0
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4
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201
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 days ago • updated 7 days ago lonn • 0
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0
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78
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
11 days ago Virangika • 0
2
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2
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150
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[DiffBind] Obtaining normalization factors
DiffBind
14 days ago • updated 10 days ago Henry ▴ 10
2
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2
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362
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
15 days ago • updated 14 days ago Henry ▴ 10
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0
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99
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
28 days ago feather-W • 0
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0
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99
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
28 days ago Ankit ▴ 20
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0
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84
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
29 days ago Pierre Lindenbaum ▴ 10
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0
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126
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
5 weeks ago erbrocato • 0
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2
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231
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago Sam ▴ 10
0
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1
reply
188
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Exact same results in Diffbind with different normalization methods
DiffBind
6 weeks ago • updated 5 weeks ago red_bricks ▴ 50
0
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1
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290
views
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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235
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
0
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0
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168
views
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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161
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
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0
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229
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
3 months ago Hai • 0
0
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0
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247
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
1
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2
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320
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
0
votes
2
replies
338
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
vote
1
reply
343
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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323
views
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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394
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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457
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
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 6 months ago by • 0
1
vote
1
reply
439
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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616
views
diffbind analyze for wheat
DiffBind
updated 8 weeks ago by • 0 • written 7 months ago by • 0
3
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7
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848
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
votes
1
reply
534
views
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
920
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by • 0 • written 8 months ago by • 0
0
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2
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460
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
1
vote
2
replies
603
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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612
views
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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805
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
0
votes
5
replies
3.0k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
vote
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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844
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
667
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
2
votes
3
replies
603
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
votes
4
replies
798
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
1
vote
2
replies
758
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
0
votes
1
reply
538
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
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0
replies
421
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
0
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0
replies
403
views
Title in dba.plotProfile
DiffBind
11 months ago agata17 • 0
8
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
1
vote
4
replies
1000
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
1
vote
0
replies
552
views
Fold values in Diffbind
DiffBind
11 months ago bhandary.8590 ▴ 20
0
votes
1
reply
651
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
2
votes
3
replies
778
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 11 months ago by • 0
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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