Showing : diffBind • reset
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68
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
7 days ago gamma.jian • 0
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2
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167
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Trouble reading samplesheet in with diffbind to create dba
DiffBind DifferentialPeakCalling
17 days ago Mallory • 0
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0
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105
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Difference in Contrast in DiffBind
DiffBind
7 weeks ago zzrammal • 0
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0
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146
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
8 weeks ago Dinesh • 0
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0
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184
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dba.plotProfile() plotting and interpretation
DiffBind
8 weeks ago Henry ▴ 10
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0
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150
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
8 weeks ago yvonneh • 0
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0
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140
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 weeks ago Ian D. ▴ 70
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6
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583
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
9 weeks ago • updated 15 days ago Ian D. ▴ 70
1
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1
reply
235
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
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1
reply
299
views
ATACseq merge peaks
DiffBind
updated 9 weeks ago by ★ 4.2k • written 10 weeks ago by • 0
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4
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336
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
11 weeks ago • updated 10 weeks ago lonn • 0
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0
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134
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
11 weeks ago Virangika • 0
2
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2
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258
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[DiffBind] Obtaining normalization factors
DiffBind
11 weeks ago Henry ▴ 10
2
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2
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508
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
11 weeks ago Henry ▴ 10
0
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0
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174
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
3 months ago feather-W • 0
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0
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169
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
3 months ago Ankit ▴ 20
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0
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162
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
3 months ago Pierre Lindenbaum ▴ 10
0
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0
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180
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
3 months ago erbrocato • 0
0
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2
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337
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
3 months ago Sam ▴ 10
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1
reply
263
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Exact same results in Diffbind with different normalization methods
DiffBind
3 months ago red_bricks ▴ 60
0
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1
reply
372
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
5 months ago isaromero8888 • 0
0
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0
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325
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
5 months ago Jawahar • 0
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0
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225
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
5 months ago frueher • 0
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0
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210
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
5 months ago Aswathy • 0
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0
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318
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
6 months ago Hai • 0
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0
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308
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
6 months ago inna.gur • 0
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1
reply
1.0k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 6 months ago by • 0 • written 10 months ago by • 0
0
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2
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425
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 6 months ago by ▴ 10
1
vote
2
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386
views
Inconsistent results in DiffBind
DiffBind
6 months ago Sam ▴ 10
1
vote
1
reply
410
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 7 months ago by ★ 4.2k • written 7 months ago by • 0
0
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0
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406
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
7 months ago jared.andrews07 ▴ 30
0
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0
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470
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 9 months ago by 66k • written 9 months ago by • 0
2
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4
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1.3k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 8 months ago by • 0 • written 9 months ago by • 0
2
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2
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522
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
9 months ago • updated 8 months ago r.murakami • 0
1
vote
1
reply
544
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 9 months ago by 66k • written 9 months ago by • 0
3
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7
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1.0k
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 9 months ago by ▴ 20
0
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3
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704
views
diffbind analyze for wheat
DiffBind
updated 4 months ago by • 0 • written 9 months ago by • 0
0
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1
reply
636
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
10 months ago Mark • 0
1
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2
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719
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
10 months ago Junsik • 0
0
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2
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548
views
DiffBind error
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
2
replies
990
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 11 months ago by ★ 1.6k • written 11 months ago by • 0
1
vote
1
reply
2.3k
views
Help with error DiffBind
DiffBind
updated 11 months ago by ★ 5.2k • written 12 months ago by ▴ 20
1
vote
1
reply
2.7k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 11 months ago by ★ 5.2k • written 11 months ago by ▴ 20
0
votes
5
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3.8k
views
diffbind
DiffBind chipseq
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
0
votes
3
replies
747
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
0
votes
5
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1.3k
views
DiffBind handling of replicates and consensus
diffbind
updated 9 months ago by ★ 5.2k • written 4.4 years ago by • 0
1
vote
4
replies
987
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
11 months ago Theo ▴ 10
1
vote
2
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758
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 12 months ago by ★ 5.2k • written 12 months ago by • 0
0
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1
reply
597
views
DiffBind output issues
DiffBind
updated 12 months ago by ★ 5.2k • written 12 months ago by • 0
1
vote
2
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914
views
Interpret plots from DiffBind
DiffBind
12 months ago Chris ▴ 20
50 results • Page 1 of 1
Recent ...
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Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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