Showing : diffBind • reset
0
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2
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919
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 23 months ago by ▴ 10
1
vote
2
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762
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Inconsistent results in DiffBind
DiffBind
23 months ago Sam ▴ 10
1
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2
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851
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 9 weeks ago by ▴ 10 • written 23 months ago by • 0
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0
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975
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
23 months ago jared.andrews07 ▴ 30
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0
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948
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
2
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4
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1.9k
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DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 2.1 years ago by ▴ 10 • written 2.1 years ago by • 0
2
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2
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882
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
2.1 years ago r.murakami • 0
1
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1
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1.2k
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
3
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7
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1.7k
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 2.1 years ago by ▴ 20
0
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3
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1.2k
views
diffbind analyze for wheat
DiffBind
updated 20 months ago by • 0 • written 2.1 years ago by • 0
0
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1
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1.1k
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
2.2 years ago Mark ▴ 10
1
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2
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1.2k
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
2.2 years ago Junsik • 0
0
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2
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904
views
DiffBind error
DiffBind
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
0
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2
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1.9k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.3 years ago by ★ 1.6k • written 2.3 years ago by • 0
1
vote
1
reply
3.9k
views
Help with error DiffBind
DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by ▴ 20
1
vote
1
reply
5.1k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by ▴ 20
0
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5
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7.4k
views
diffbind
DiffBind chipseq
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by • 0
0
votes
3
replies
1.2k
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by • 0
0
votes
5
replies
2.3k
views
DiffBind handling of replicates and consensus
diffbind
updated 2.1 years ago by ★ 5.2k • written 5.7 years ago by • 0
1
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4
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1.7k
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
2.3 years ago Theo ▴ 10
1
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2
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1.1k
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by • 0
0
votes
1
reply
1.0k
views
DiffBind output issues
DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
1
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2
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1.5k
views
Interpret plots from DiffBind
DiffBind
2.4 years ago Chris ▴ 20
2
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3
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1.3k
views
Sample sheet file for DiffBind
DiffBind
updated 22 months ago by • 0 • written 2.4 years ago by ▴ 20
4
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4
replies
1.6k
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
2.4 years ago bhandary.8590 ▴ 20
1
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0
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673
views
Help with error running DiffBind
DiffBind
2.4 years ago Chris ▴ 20
1
vote
7
replies
2.3k
views
Diffbind "No genome detected"
DiffBind
updated 23 months ago by 68k • written 2.4 years ago by • 0
8
votes
13
replies
3.4k
views
Interpret plot from DiffBind
DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by ▴ 20
0
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0
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644
views
Title in dba.plotProfile
DiffBind
2.4 years ago agata17 • 0
0
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1
reply
886
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 2.4 years ago by ★ 5.2k • written 2.5 years ago by ▴ 10
0
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1
reply
1.2k
views
DiffBind dba() in parallel
DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
1
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4
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2.2k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
1
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0
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1.0k
views
Fold values in Diffbind
DiffBind
2.4 years ago bhandary.8590 ▴ 20
2
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3
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1.2k
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 2.4 years ago by • 0
0
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0
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783
views
Help with Diffbind result
DiffBind
2.5 years ago Chris ▴ 20
3
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5
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4.0k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
updated 3 months ago by • 0 • written 2.5 years ago by ▴ 10
0
votes
7
replies
2.3k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
2.5 years ago • updated 2.4 years ago Ti • 0
2
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1
reply
1.1k
views
how diffbind count the reads of each peak in each sample?
diffbind DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
4
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6
replies
1.7k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.5 years ago Chris ▴ 20
0
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1
reply
945
views
Plotting read densities from DiffBind results
Read density DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by ▴ 20
0
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2
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1.1k
views
Question regarding multiple comparisons in DiffBind
DiffBind
2.6 years ago • updated 2.5 years ago epipally • 0
8
votes
13
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5.4k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.6 years ago Chris ▴ 20
0
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2
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1.4k
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by • 0
0
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2
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2.0k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
0
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0
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820
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
1
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3
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1.1k
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by • 0
1
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2
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1.0k
views
DiffBind spike-in lib.sizes confusion
SpikeIn DiffBind
2.7 years ago • updated 2.6 years ago Weisheng • 0
0
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13
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2.8k
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze DiffBind @rory-stark-5741
2.6 years ago tahir.msajid • 0
0
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1
reply
683
views
DiffBind---peak region reads or all reads？
DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
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0
replies
703
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Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind MeRIP-seq m6A-seq
2.7 years ago zhiyi • 0
678 results • Page 2 of 14
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Yes, limma can definitely be used with module eigengenes instead of individual genes. As Gordon Smyth mentioned, since eigengenes represent…
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It's obvious that the blogger hought on details. It is not only easy to read but also makes the content more rich and interesting.[1v1 …
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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