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3
votes
1
answer
135
views
1
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Alternative/Incorrect DiffBind outputs for each contrast when providing entire vs. partial datasheet
software error diffbind chip-seq written 4 weeks ago by gkunz • 10 • updated 4 weeks ago by jared.andrews07 ♦ 7.5k
5
votes
1
answer
155
views
1
answer
how matrix composition influences the final results in diff bind
diffbind chip-seq written 6 weeks ago by francesca3 • 30 • updated 6 weeks ago by Rory Stark • 790
0
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0
answers
142
views
0
answers
ChIP-seq Differential Binding analysis for specified genomic regions of interest? (DiffBind/csaw?)
csaw R diffbind differential binding chip-seq written 8 weeks ago by jennxyzhang • 0 • updated 8 weeks ago by ATpoint ♦ 40k
0
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0
answers
161
views
0
answers
Combining the original replicates and pseudo-replicates for differential binding analysis?
replicates R diffbind chip-seq written 11 weeks ago by maisarasora • 10
0
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1
answer
112
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1
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diffBind dba.count error for a peaks file selected
diffbind chip-seq written 3 months ago by iridha • 0 • updated 3 months ago by Rory Stark • 790
2
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2
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154
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2
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Extract RPKM values from Diffbind
rpkm diffbind chip-seq written 3 months ago by francesca3 • 30 • updated 3 months ago by Rory Stark • 790
0
votes
1
answer
123
views
1
answer
why DiffBind, diffferentially binding site is the for different samples
diffbind alignment chip-seq written 3 months ago by iridha • 0 • updated 3 months ago by Rory Stark • 790
0
votes
1
answer
284
views
1
answer
How to make complex contrasts in DiffBind dba.contrast
R diffbind tool dba.contrast written 4 months ago by Bioinformatist Newbie • 250 • updated 3 months ago by Rory Stark • 790
3
votes
2
answers
341
views
2
answers
Difference of DiffBind library size normalisation vs DESeq2 library size normalisation
diffbind deseq2 chip-seq rna-seq normalisation written 5 months ago by bioinfouser • 70 • updated 5 months ago by Rory Stark • 790
1
vote
1
answer
265
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1
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Diffbind- results different every time I run it
software error diffbind written 7 months ago by francesca3 • 30 • updated 5 months ago by Michael Dondrup ♦ 47k
2
votes
1
answer
260
views
1
answer
Obtained too many chip-seq peaks after diffbind, how to set a criteria to select more "significant" genes?
diffbind chip-seq written 5 months ago by yepeh72919 • 10 • updated 5 months ago by Rory Stark • 790
0
votes
1
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1.5k
views
1
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Error while annotating with Chipseeker
chip-seq diffbind chipseeker annotation written 20 months ago by hamaor • 0 • updated 9 months ago by michal.okoniewski • 0
0
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0
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240
views
0
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Changing the color of significantly up- or downregulated peaks in volcano plot from Diffbind
volcano diffbind volcano plot written 9 months ago by collmerr • 40
0
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0
answers
210
views
0
answers
How to make a read count matrix from multiple bed files generated by ROSE
rose chipseq diffbind h3k27ac super-enhancers written 11 months ago by Researcher • 60
10
votes
3
answers
562
views
6 follow
3
answers
DiffBind to call differential binding of Super-enhancers from ROSE
rose chipseq diffbind super-enhancers written 12 months ago by Researcher • 60 • updated 12 months ago by sim.j.baum • 50
2
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2
answers
935
views
6 follow
2
answers
DiffBind without replicates
R diffbind chip-seq written 12 months ago by zhangdengwei • 130
1
vote
1
answer
797
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1
answer
Which method is the best for using in "dba.count" in Diffbind R package
diffbind chip-seq written 12 months ago by bioinfouser • 70 • updated 12 months ago by Rory Stark • 790
0
votes
0
answers
278
views
0
answers
ChIP-seq differential binding analysis tools
csaw diffbind chip-seq written 12 months ago by Jingyue • 30
3
votes
1
answer
910
views
1
answer
Are MACS2's summit or DiffBind's summit options are recommended for histone marks like H3K4me3, H3K27me3, H3K27ac and H3K4me1?
diffbind macs2 chip-seq summit histone written 13 months ago by Researcher • 60 • updated 13 months ago by Rory Stark • 790
0
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0
answers
407
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0
answers
Exploring H3K27me3 loss in cancer
h3k27me3 diffbind macs2 chip-seq histone written 13 months ago by Researcher • 60
0
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1
answer
874
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1
answer
Diffbind error : sequences from an unspecified genome; no seqlengths
macs diffbind macs2 chip-seq granges written 2.6 years ago by erwan.scaon • 810 • updated 15 months ago by kieran.short • 0
0
votes
1
answer
732
views
1
answer
DiffBind package showing warnings and unable to analyse my data
diffbind chip-seq written 15 months ago by chaudharyc61 • 30 • updated 15 months ago by Rory Stark • 790
0
votes
0
answers
209
views
0
answers
diffbind dba.plotvolcano bLabels option use genames instead of numbers
volcano diffbind written 16 months ago by theodore • 80
4
votes
1
answer
743
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1
answer
How to properly organize a DiffBind analysis to normalize data across conditions (ChIP-seq)
R diffbind chip-seq written 17 months ago by msimmer92 • 260 • updated 17 months ago by ATpoint ♦ 40k
0
votes
1
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276
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1
answer
Diffbind affinity based analysis
diffbind chip-seq affinity analysis written 17 months ago by rapmic • 0 • updated 17 months ago by Rory Stark • 790
2
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2
answers
1.6k
views
2
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Convert DiffBind output to standard BED or NarrowPeak format
bed diffbind chip-seq narrowpeak written 3.1 years ago by rbronste • 360 • updated 18 months ago by corinne_hutfilz • 0
0
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2
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1.1k
views
2
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how to retrieve binding affinity matrix in diffbind
diffbind dba.count chip-seq written 20 months ago by hamaor • 0 • updated 19 months ago by Rory Stark • 790
3
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0
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3.3k
views
0
answers
DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
R diffbind chip-seq written 19 months ago by msimmer92 • 260
1
vote
0
answers
530
views
0
answers
extract some feature from peak?
bedtools featurecount diffbind macs2 chip-seq written 19 months ago by star • 260
0
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1
answer
741
views
1
answer
R's DiffBind. Error in pv.DBAplotVolcano(DBA, contrast = contrast, method = method,: object 'sigSites' not found
R diffbind chip-seq written 20 months ago by msimmer92 • 260 • updated 20 months ago by Friederike ♦ 6.3k
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