Showing : diffBind • reset
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Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind MeRIP-seq m6A-seq
2.9 years ago zhiyi • 0
1
vote
1
reply
2.1k
views
DiffBind differential analysis
DifferentialPeakCalling ChIPanalyser DiffBind chipseqDB
updated 3.0 years ago by ★ 5.3k • written 3.0 years ago by • 0
1
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3
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1.7k
views
DiffBind---Normalization problem-spike in or no spike in beforehand?
DiffBind
updated 3.0 years ago by ★ 5.3k • written 3.0 years ago by • 0
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1
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1.3k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 3.0 years ago by ★ 5.3k • written 3.0 years ago by • 0
0
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1
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1.0k
views
Setting DBA$config$mergeOverlap for Diffbind
DiffBind
updated 3.0 years ago by ★ 5.3k • written 3.0 years ago by • 0
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2
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921
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 3.1 years ago by ★ 5.3k • written 3.1 years ago by • 0
0
votes
7
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1.9k
views
Issue in generating a new DBA object with custom counts
DiffBind dbaobject
3.2 years ago • updated 3.1 years ago francesco.gandolfi • 0
0
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1
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1.5k
views
Diffbind matrix/batch effect/normalization
DiffBind
updated 3.1 years ago by ★ 5.3k • written 3.2 years ago by ▴ 10
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8
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2.1k
views
Question about Diffbind counts
DiffBind
3.1 years ago slrpatty • 0
0
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3
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1.5k
views
Minor issue regarding customization of text size in Volcano and Heatmap Plots
DiffBind
updated 3.1 years ago by ★ 5.3k • written 3.2 years ago by ▴ 10
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1
reply
819
views
dba.count Error in DiffBind
DiffBind
3.1 years ago narzouni • 0
3
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4
replies
3.3k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
3.2 years ago • updated 3.1 years ago spg • 0
0
votes
1
reply
1.4k
views
DiffBind: Error in pv$called[, mask] : subscript out of bounds
DiffBind
updated 3.2 years ago by ★ 5.3k • written 3.2 years ago by • 0
1
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2
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1.2k
views
DiffBind Loss and Gain location
DiffBind
updated 3.1 years ago by ★ 5.3k • written 3.2 years ago by • 0
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3
replies
2.1k
views
Blacklist error in DiffBind
DiffBind Blacklist
updated 23 months ago by • 0 • written 3.3 years ago by • 0
2
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1
reply
1.1k
views
Error in DiffBind dba.blacklist & dba.count
DiffBind
updated 3.3 years ago by ★ 5.3k • written 3.3 years ago by • 0
2
votes
1
reply
1.1k
views
Different sequencing depth between replicates and samples
DESeq2 edgeR DiffBind
updated 3.3 years ago by 53k • written 3.3 years ago by ▴ 10
2
votes
13
replies
4.3k
views
Too much data for Diffbind
DiffBind
updated 16 months ago by ★ 1.3k • written 3.3 years ago by ▴ 10
2
votes
4
replies
1.8k
views
DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 3.2 years ago by ★ 5.3k • written 3.3 years ago by ▴ 670
1
vote
25
replies
6.2k
views
DiffBind spike-in normalization
DiffBind
3.3 years ago yuhuihui2011 • 0
0
votes
1
reply
1.4k
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 3.3 years ago by ★ 5.3k • written 3.4 years ago by • 0
2
votes
4
replies
4.3k
views
Normalizing Cut&Tag peak data
Normalization Peakdata DiffBind Cut&Tag
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by ▴ 20
1
vote
3
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1.4k
views
Issue carrying out DiffBind Analysis at a predefined peak set
DiffBind
updated 3.4 years ago by ★ 5.3k • written 3.4 years ago by • 0
2
votes
1
reply
2.3k
views
DiffBind: Error in if (res$config$bCorPlot) { : the condition has length > 1
DiffBind ChIPQC
updated 3.4 years ago by ★ 5.3k • written 3.5 years ago by • 0
0
votes
7
replies
3.0k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.5 years ago by ▴ 40 • written 5.8 years ago by ▴ 10
1
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2
replies
1.6k
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
3.6 years ago • updated 3.5 years ago etiennedanis • 0
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2
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1.5k
views
DESeq2 analysis has not been run for this contrast
R DiffBind
3.6 years ago Wang • 0
0
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1
reply
1.3k
views
DiffBind: dba.plotPCA() ellipse
PrincipalComponent DiffBind
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by • 0
1
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3
replies
1.5k
views
Low Differentially Bound Sites found with DiffBind
Cut&Run DiffBind
3.6 years ago gannoncottone • 0
0
votes
1
reply
2.2k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 3.6 years ago by ★ 5.3k • written 3.7 years ago by • 0
0
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1
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1.9k
views
During dba(sampleSheet = "samples.csv") step, Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=charac…
DiffBind
updated 3.6 years ago by ★ 5.3k • written 3.6 years ago by • 0
0
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1
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1.7k
views
DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
DiffBind
updated 3.6 years ago by ★ 5.3k • written 3.7 years ago by ▴ 10
0
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0
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656
views
diffbind dba.report
diffbind
3.7 years ago jonathanho1989 • 0
0
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0
replies
924
views
diffbind dba.count error
peakfiles diffbind HMMRATAC
3.7 years ago jonathanho1989 • 0
0
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0
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747
views
Diffbind not calling sites as differentially bound
DiffBind
3.7 years ago ipsc-jl • 0
0
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1
reply
1.1k
views
Diffbind: different results on the same sample depending on contrast parameters
DifferentialExpression DiffBind
updated 3.7 years ago by ★ 5.3k • written 3.7 years ago by • 0
0
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0
replies
865
views
How to set $control.subtract to FALSE in DiffBind?
DiffBind
3.7 years ago ksong ▴ 10
0
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3
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1.7k
views
DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change introduced between version 2.14 and 3.4.11
DiffBind
updated 3.8 years ago by ★ 5.3k • written 3.8 years ago by • 0
2
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5
replies
1.4k
views
Diffbind dba$binding slot finding Chr21 for an MM10 dataset
DiffBind
updated 3.8 years ago by • 0 • written 3.8 years ago by • 0
0
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3
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1.8k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3.8 years ago by ★ 5.3k • written 3.8 years ago by • 0
2
votes
3
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1.7k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.8 years ago • updated 3.7 years ago bers.anthrope ▴ 10
0
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3
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1.8k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
written 3.9 years ago by • 0
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0
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786
views
DiffBind does not load samples
DiffBind
3.9 years ago nw416 • 0
3
votes
6
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3.3k
views
Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind dba.plotPCA
updated 3.5 years ago by • 0 • written 4.8 years ago by ▴ 10
1
vote
1
reply
2.1k
views
DiffBind drop out some peaks
DiffBind
updated 3.9 years ago by ★ 5.3k • written 3.9 years ago by • 0
0
votes
0
replies
999
views
Creating a consensus peakset in DiffBind for all the conditions of an experiment
DiffBind
3.9 years ago Sam ▴ 10
2
votes
2
replies
5.0k
views
BiocParallel error when running DiffBind
BiocParallel BiocPa DiffBind
updated 3.9 years ago by 25k • written 4.0 years ago by ▴ 10
0
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0
replies
1.3k
views
DiffBind error
DiffBind DifferentialPeakCalling
3.9 years ago Amandeep • 0
0
votes
1
reply
832
views
DiffBind contrast design - pairwise with independent filtering
DiffBind
updated 3.8 years ago by • 0 • written 3.9 years ago by • 0
0
votes
9
replies
4.4k
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
5.2 years ago • updated 4.0 years ago Tongjun • 0
679 results • Page 3 of 14
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Answer: Unable to create venndiagram using VennDiagram 1.5.1 package by kesha • 0
<a href=https://vavadacasinox.com/>vavadacasinox.com</a>
Comment: How to convert .raw data for use in xcms by a2a2asawhaa • 0
try converting your files to the older mzXML format, which remains highly stable for XCMS. While waiting for large datasets to process, you…
Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
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A: Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE metho
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
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