Showing : diffbind • reset
2
votes
2
replies
2.1k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 9 months ago by • 0 • written 2.5 years ago by ▴ 10
0
votes
2
replies
1.0k
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 2.2 years ago by ▴ 10
1
vote
2
replies
836
views
Inconsistent results in DiffBind
DiffBind
2.2 years ago Sam ▴ 10
1
vote
2
replies
940
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 5 months ago by ▴ 10 • written 2.2 years ago by • 0
0
votes
0
replies
1.1k
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
2.2 years ago jared.andrews07 ▴ 30
0
votes
0
replies
1.0k
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
2
votes
4
replies
2.0k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 2.3 years ago by ▴ 10 • written 2.3 years ago by • 0
2
votes
2
replies
963
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
2.3 years ago r.murakami • 0
1
vote
1
reply
1.3k
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
3
votes
7
replies
1.8k
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 2.4 years ago by ▴ 20
0
votes
3
replies
1.3k
views
diffbind analyze for wheat
DiffBind
updated 23 months ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
1.2k
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
2.5 years ago Mark ▴ 10
1
vote
2
replies
1.4k
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
2.5 years ago Junsik • 0
0
votes
2
replies
954
views
DiffBind error
DiffBind
updated 2.5 years ago by ★ 5.3k • written 2.5 years ago by • 0
0
votes
2
replies
2.3k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
1
vote
1
reply
4.0k
views
Help with error DiffBind
DiffBind
updated 2.5 years ago by ★ 5.3k • written 2.6 years ago by ▴ 20
1
vote
1
reply
5.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 2.5 years ago by ★ 5.3k • written 2.6 years ago by ▴ 20
0
votes
5
replies
7.5k
views
diffbind
DiffBind chipseq
updated 2.5 years ago by ★ 5.3k • written 2.5 years ago by • 0
0
votes
3
replies
1.4k
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 2.5 years ago by ★ 5.3k • written 2.5 years ago by • 0
0
votes
5
replies
2.4k
views
DiffBind handling of replicates and consensus
diffbind
updated 2.4 years ago by ★ 5.3k • written 6.0 years ago by • 0
1
vote
4
replies
1.8k
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
2.6 years ago Theo ▴ 10
1
vote
2
replies
1.2k
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 2.6 years ago by ★ 5.3k • written 2.6 years ago by • 0
0
votes
1
reply
1.1k
views
DiffBind output issues
DiffBind
updated 2.6 years ago by ★ 5.3k • written 2.7 years ago by • 0
1
vote
2
replies
1.5k
views
Interpret plots from DiffBind
DiffBind
2.7 years ago • updated 2.6 years ago Chris ▴ 20
2
votes
3
replies
1.5k
views
Sample sheet file for DiffBind
DiffBind
updated 2.1 years ago by • 0 • written 2.6 years ago by ▴ 20
4
votes
4
replies
1.8k
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
2.6 years ago bhandary.8590 ▴ 20
1
vote
0
replies
698
views
Help with error running DiffBind
DiffBind
2.7 years ago Chris ▴ 20
1
vote
7
replies
2.5k
views
Diffbind "No genome detected"
DiffBind
updated 2.2 years ago by 68k • written 2.7 years ago by • 0
8
votes
13
replies
3.7k
views
Interpret plot from DiffBind
DiffBind
updated 2.7 years ago by ★ 5.3k • written 2.7 years ago by ▴ 20
0
votes
0
replies
678
views
Title in dba.plotProfile
DiffBind
2.7 years ago agata17 • 0
0
votes
1
reply
936
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 2.7 years ago by ★ 5.3k • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.3k
views
DiffBind dba() in parallel
DiffBind
updated 2.7 years ago by ★ 5.3k • written 2.7 years ago by • 0
1
vote
4
replies
2.5k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.7 years ago by ★ 5.3k • written 2.7 years ago by • 0
1
vote
0
replies
1.1k
views
Fold values in Diffbind
DiffBind
2.7 years ago bhandary.8590 ▴ 20
2
votes
3
replies
1.3k
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 2.7 years ago by • 0
0
votes
0
replies
824
views
Help with Diffbind result
DiffBind
2.7 years ago Chris ▴ 20
3
votes
5
replies
4.3k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
updated 6 months ago by • 0 • written 2.8 years ago by ▴ 10
0
votes
7
replies
2.4k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
2.8 years ago • updated 2.7 years ago Ti • 0
2
votes
1
reply
1.2k
views
how diffbind count the reads of each peak in each sample?
diffbind DiffBind
updated 2.8 years ago by ★ 5.3k • written 2.8 years ago by • 0
4
votes
6
replies
1.8k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.8 years ago Chris ▴ 20
0
votes
1
reply
998
views
Plotting read densities from DiffBind results
Read density DiffBind
updated 2.8 years ago by ★ 5.3k • written 2.8 years ago by ▴ 20
0
votes
2
replies
1.2k
views
Question regarding multiple comparisons in DiffBind
DiffBind
2.8 years ago epipally • 0
8
votes
13
replies
5.7k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.9 years ago Chris ▴ 20
0
votes
2
replies
1.5k
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 2.9 years ago by ★ 5.3k • written 2.9 years ago by • 0
0
votes
2
replies
2.2k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.9 years ago Giulia • 0
0
votes
0
replies
870
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.9 years ago Giulia • 0
1
vote
3
replies
1.2k
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 2.9 years ago by ★ 5.3k • written 2.9 years ago by • 0
1
vote
2
replies
1.1k
views
DiffBind spike-in lib.sizes confusion
SpikeIn DiffBind
2.9 years ago Weisheng • 0
0
votes
13
replies
3.1k
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze DiffBind @rory-stark-5741
2.9 years ago tahir.msajid • 0
0
votes
1
reply
728
views
DiffBind---peak region reads or all reads？
DiffBind
updated 2.9 years ago by ★ 5.3k • written 2.9 years ago by • 0
679 results • Page 2 of 14
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Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Votes
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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