Showing : diffbind • reset
5
votes
19
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6.0k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by • 0 • written 2.8 years ago by ▴ 10
0
votes
5
replies
3.2k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
vote
7
replies
3.0k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
1
vote
1
reply
2.4k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 10 months ago by ▴ 20
1
vote
1
reply
2.0k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by ▴ 10
0
votes
4
replies
2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 3 months ago by ★ 5.2k • written 7.9 years ago by • 0
8
votes
13
replies
2.0k
views
Interpret plot from DiffBind
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by ▴ 10
1
vote
3
replies
1.9k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 5 months ago by ★ 5.2k • written 6.6 years ago by • 0
0
votes
7
replies
1.4k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
13 months ago • updated 11 months ago Ti • 0
0
votes
5
replies
1.4k
views
DiffBind:all samples have 0 counts for all genes.
DiffBind Genrich
updated 11 months ago by • 0 • written 3.5 years ago by • 0
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 3 months ago by • 0 • written 2.4 years ago by • 0
2
votes
4
replies
1.3k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 7 months ago by • 0 • written 7 months ago by • 0
1
vote
7
replies
1.3k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
0
votes
5
replies
1.2k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by ★ 5.2k • written 4.3 years ago by • 0
0
votes
3
replies
1.2k
views
Blacklist error in DiffBind
DiffBind Blacklist
updated 10 weeks ago by • 0 • written 18 months ago by • 0
2
votes
3
replies
1.2k
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
vote
4
replies
1.1k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 11 months ago by ★ 5.2k • written 12 months ago by • 0
1
vote
4
replies
1.0k
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by • 0
0
votes
1
reply
958
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
vote
4
replies
908
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 months ago Theo ▴ 10
3
votes
7
replies
884
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
0
votes
2
replies
879
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
4
votes
4
replies
848
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
11 months ago • updated 10 months ago bhandary.8590 ▴ 20
1
vote
2
replies
828
views
Interpret plots from DiffBind
DiffBind
11 months ago • updated 10 months ago Chris ▴ 10
2
votes
3
replies
808
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 12 months ago by • 0
1
vote
2
replies
712
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
1
reply
697
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.2k • written 12 months ago by • 0
0
votes
3
replies
675
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
1
vote
2
replies
658
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago Junsik • 0
0
votes
3
replies
658
views
diffbind analyze for wheat
DiffBind
updated 11 weeks ago by • 0 • written 8 months ago by • 0
2
votes
3
replies
655
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
1
vote
0
replies
589
views
Fold values in Diffbind
DiffBind
12 months ago bhandary.8590 ▴ 20
0
votes
1
reply
575
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 11 months ago by ★ 5.2k • written 12 months ago by ▴ 10
0
votes
1
reply
570
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago Mark • 0
0
votes
1
reply
565
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
0
votes
2
replies
510
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 9 months ago by • 0
2
votes
2
replies
486
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 0
1
vote
1
reply
472
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
0
votes
0
replies
445
views
Help with error running DiffBind
DiffBind
11 months ago Chris ▴ 10
0
votes
0
replies
429
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
2
votes
2
replies
418
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
5 weeks ago Henry ▴ 10
0
votes
0
replies
418
views
Title in dba.plotProfile
DiffBind
11 months ago agata17 • 0
0
votes
2
replies
379
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
1
vote
1
reply
377
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
0
votes
4
replies
376
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 7 days ago by • 0 • written 18 days ago by ▴ 70
1
vote
2
replies
352
views
Inconsistent results in DiffBind
DiffBind
5 months ago Sam ▴ 10
0
votes
0
replies
351
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
6 months ago jared.andrews07 ▴ 30
0
votes
1
reply
327
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
votes
0
replies
282
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
0
votes
2
replies
276
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago Sam ▴ 10
50 results • Page 1 of 1
Recent ...
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Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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