Showing : diffBind • reset
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26
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dba.plotProfile() plotting and interpretation
DiffBind
16 hours ago Henry ▴ 10
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0
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34
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
1 day ago yvonneh • 0
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0
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27
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
1 day ago Ian D. ▴ 70
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2
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105
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 1 day ago Ian D. ▴ 70
1
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1
reply
93
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
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1
reply
123
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ATACseq merge peaks
DiffBind
updated 7 days ago by ★ 4.1k • written 9 days ago by • 0
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4
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234
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
16 days ago • updated 14 days ago lonn • 0
2
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2
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170
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[DiffBind] Obtaining normalization factors
DiffBind
21 days ago • updated 18 days ago Henry ▴ 10
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0
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94
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
18 days ago Virangika • 0
2
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2
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384
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
22 days ago • updated 21 days ago Henry ▴ 10
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0
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110
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
5 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
5 weeks ago Ankit ▴ 20
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0
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96
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
5 weeks ago Pierre Lindenbaum ▴ 10
0
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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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1
reply
197
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Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago red_bricks ▴ 50
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2
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244
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
0
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3
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1.1k
views
Blacklist error in DiffBind
DiffBind Blacklist
updated 7 weeks ago by • 0 • written 17 months ago by • 0
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3
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632
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diffbind analyze for wheat
DiffBind
updated 9 weeks ago by • 0 • written 7 months ago by • 0
2
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4
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1.3k
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DiffBind: dba.plotProfile(profiles)
DiffBind
updated 11 weeks ago by • 0 • written 2.4 years ago by • 0
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4
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2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 3 months ago by ★ 5.2k • written 7.8 years ago by • 0
1
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7
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2.9k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
0
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1
reply
299
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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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176
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
1
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4
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993
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Diffbind error while running example data
DiffBind
written 3.2 years ago by • 0
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
2
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3
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615
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Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
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0
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238
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
4 months ago Hai • 0
0
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0
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257
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
0
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1
reply
933
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by • 0 • written 8 months ago by • 0
1
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3
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1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 4 months ago by ★ 5.2k • written 6.6 years ago by • 0
1
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2
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326
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Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
0
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2
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352
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
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1
reply
354
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.1k • written 5 months ago by • 0
1
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7
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1.2k
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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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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
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
2
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2
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466
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago • updated 6 months ago r.murakami • 0
0
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0
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408
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 7 months ago by 65k • written 7 months ago by • 0
0
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5
replies
1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by ★ 5.2k • written 4.2 years ago by • 0
1
vote
1
reply
449
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
3
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7
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861
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
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1
reply
543
views
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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624
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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2
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484
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
5
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19
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5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by • 0 • written 2.8 years ago by ▴ 10
0
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2
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836
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • 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 10 months ago by • 0
2
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3
replies
1.1k
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 9 months ago by ★ 5.2k • written 3.1 years ago by ▴ 10
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
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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