Showing : diffbind • reset
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942
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 24 months ago by ▴ 10
1
vote
2
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783
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Inconsistent results in DiffBind
DiffBind
24 months ago Sam ▴ 10
1
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2
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871
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 3 months ago by ▴ 10 • written 24 months ago by • 0
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0
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1.0k
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
2.0 years ago jared.andrews07 ▴ 30
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0
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968
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
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4
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1.9k
views
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 2.2 years ago by • 0
2
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2
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906
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
2.2 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 2.2 years ago by 68k • written 2.2 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 2.2 years ago by ▴ 20
0
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3
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1.2k
views
diffbind analyze for wheat
DiffBind
updated 21 months ago by • 0 • written 2.2 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
2.3 years ago Mark ▴ 10
1
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2
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1.3k
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
2.3 years ago Junsik • 0
0
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2
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916
views
DiffBind error
DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.3 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 2.4 years ago by ★ 1.6k • written 2.4 years ago by • 0
1
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1
reply
3.9k
views
Help with error DiffBind
DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by ▴ 20
1
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1
reply
5.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by ▴ 20
0
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5
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7.4k
views
diffbind
DiffBind chipseq
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
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3
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1.2k
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
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5
replies
2.3k
views
DiffBind handling of replicates and consensus
diffbind
updated 2.2 years ago by ★ 5.2k • written 5.8 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
2.4 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 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
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1
reply
1.0k
views
DiffBind output issues
DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.5 years ago by • 0
1
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2
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1.5k
views
Interpret plots from DiffBind
DiffBind
2.5 years ago • updated 2.4 years ago Chris ▴ 20
2
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3
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1.4k
views
Sample sheet file for DiffBind
DiffBind
updated 23 months ago by • 0 • written 2.4 years ago by ▴ 20
4
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4
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1.6k
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
2.5 years ago • updated 2.4 years ago bhandary.8590 ▴ 20
1
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0
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681
views
Help with error running DiffBind
DiffBind
2.5 years ago Chris ▴ 20
1
vote
7
replies
2.4k
views
Diffbind "No genome detected"
DiffBind
updated 2.0 years ago by 68k • written 2.5 years ago by • 0
8
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13
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3.5k
views
Interpret plot from DiffBind
DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by ▴ 20
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0
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652
views
Title in dba.plotProfile
DiffBind
2.5 years ago agata17 • 0
0
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1
reply
898
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 2.5 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 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
1
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4
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2.3k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
1
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0
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1.0k
views
Fold values in Diffbind
DiffBind
2.5 years ago bhandary.8590 ▴ 20
2
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3
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1.3k
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 2.5 years ago by • 0
0
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0
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793
views
Help with Diffbind result
DiffBind
2.5 years ago Chris ▴ 20
3
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5
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4.1k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
updated 4 months ago by • 0 • written 2.6 years ago by ▴ 10
0
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7
replies
2.3k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
2.6 years ago • updated 2.5 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 2.6 years ago by ★ 5.2k • written 2.6 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
2.6 years ago Chris ▴ 20
0
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1
reply
965
views
Plotting read densities from DiffBind results
Read density DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.7 years ago by ▴ 20
0
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2
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1.2k
views
Question regarding multiple comparisons in DiffBind
DiffBind
2.7 years ago • updated 2.6 years ago epipally • 0
8
votes
13
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5.4k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.7 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 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
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2
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2.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
0
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0
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833
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
1
vote
3
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1.1k
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.7 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 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
2.7 years ago tahir.msajid • 0
0
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1
reply
695
views
DiffBind---peak region reads or all reads？
DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.8 years ago by • 0
0
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0
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722
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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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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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