Showing : diffbind • reset
3
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7
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 14 days ago by • 0
0
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2
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177
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diffbind analyze for wheat
DiffBind
13 days ago zgyu12 • 0
0
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1
reply
195
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Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
4 weeks ago Mark • 0
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0
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133
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DiffBind; Error: No sites have activity greater than filter value
DiffBind
4 weeks ago Mark • 0
1
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2
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204
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DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
7 weeks ago • updated 4 weeks ago Junsik • 0
0
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2
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165
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DiffBind error
DiffBind
updated 4 weeks ago by ★ 5.0k • written 6 weeks ago by • 0
0
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2
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305
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 8 weeks ago by ★ 1.6k • written 9 weeks ago by • 0
1
vote
1
reply
447
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Help with error DiffBind
DiffBind
updated 8 weeks ago by ★ 5.0k • written 12 weeks ago by • 0
0
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1
reply
422
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Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 weeks ago by ★ 5.0k • written 10 weeks ago by • 0
0
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5
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415
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diffbind
DiffBind chipseq
updated 9 weeks ago by ★ 5.0k • written 9 weeks ago by • 0
0
votes
3
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248
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DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 9 weeks ago by ★ 5.0k • written 9 weeks ago by • 0
0
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4
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625
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DiffBind handling of replicates and consensus
diffbind
updated 5 weeks ago by • 0 • written 3.6 years ago by • 0
0
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4
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360
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diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 weeks ago Theo • 0
1
vote
2
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344
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 11 weeks ago by ★ 5.0k • written 11 weeks ago by • 0
0
votes
1
reply
224
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DiffBind output issues
DiffBind
updated 3 months ago by ★ 5.0k • written 3 months ago by • 0
1
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2
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328
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Interpret plots from DiffBind
DiffBind
3 months ago Chris • 0
2
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2
replies
264
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Sample sheet file for DiffBind
DiffBind
updated 11 weeks ago by • 0 • written 3 months ago by • 0
4
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4
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365
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DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
3 months ago bhandary.8590 • 0
0
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0
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188
views
Help with error running DiffBind
DiffBind
3 months ago Chris • 0
1
vote
5
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541
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Diffbind "No genome detected"
DiffBind
3 months ago kyliecode • 0
7
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13
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918
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Interpret plot from DiffBind
DiffBind
updated 3 months ago by ★ 5.0k • written 4 months ago by • 0
0
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0
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168
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Title in dba.plotProfile
DiffBind
3 months ago agata17 • 0
0
votes
1
reply
283
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 4 months ago by ★ 5.0k • written 4 months ago by ▴ 10
0
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1
reply
306
views
DiffBind dba() in parallel
DiffBind
updated 4 months ago by ★ 5.0k • written 4 months ago by • 0
1
vote
4
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473
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 3 months ago by ★ 5.0k • written 4 months ago by • 0
0
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0
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191
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Fold values in Diffbind
DiffBind
4 months ago bhandary.8590 • 0
0
votes
3
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418
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 4 months ago by • 0
0
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0
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231
views
Help with Diffbind result
DiffBind
4 months ago Chris • 0
3
votes
4
replies
782
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
4 months ago Mark • 0
0
votes
7
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775
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DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
5 months ago • updated 3 months ago Ti • 0
2
votes
1
reply
275
views
how diffbind count the reads of each peak in each sample?
diffbind DiffBind
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
votes
5
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613
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DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 4 months ago by • 0 • written 5 months ago by • 0
4
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6
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563
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
5 months ago Chris • 0
0
votes
1
reply
293
views
Plotting read densities from DiffBind results
Read density DiffBind
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
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2
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390
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Question regarding multiple comparisons in DiffBind
DiffBind
5 months ago epipally • 0
8
votes
13
replies
1.4k
views
Help with Error in DiffBind
DiffBind ATACSeq
6 months ago • updated 5 months ago Chris • 0
0
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2
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452
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
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2
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525
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
6 months ago Giulia • 0
0
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0
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215
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
6 months ago Giulia • 0
1
vote
3
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338
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Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
1
vote
2
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307
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DiffBind spike-in lib.sizes confusion
SpikeIn DiffBind
6 months ago Weisheng • 0
0
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13
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853
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Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze DiffBind @rory-stark-5741
6 months ago tahir.msajid • 0
0
votes
1
reply
263
views
DiffBind---peak region reads or all reads？
DiffBind
updated 6 months ago by ★ 5.0k • written 7 months ago by • 0
0
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0
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194
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind MeRIP-seq m6A-seq
6 months ago zhiyi • 0
0
votes
1
reply
412
views
DiffBind differential analysis
DifferentialPeakCalling ChIPanalyser DiffBind chipseqDB
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
1
vote
3
replies
545
views
DiffBind---Normalization problem-spike in or no spike in beforehand?
DiffBind
updated 6 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
345
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
1
reply
329
views
Setting DBA$config$mergeOverlap for Diffbind
DiffBind
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
2
replies
381
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
votes
7
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746
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Issue in generating a new DBA object with custom counts
DiffBind dbaobject
9 months ago • updated 8 months ago francesco.gandolfi • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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