Showing : diffBind • reset
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1.4k
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DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by • 0
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598
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DiffBind 2.10.0: Consensus peaks seems to miss 2/3 of original sample peaks
DiffBind Consensus peak
updated 5.8 years ago by ★ 5.2k • written 5.9 years ago by • 0
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2
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1.2k
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DiffBind: error with dba.peakset()
DiffBind Peakset
updated 5.8 years ago by ★ 5.2k • written 5.9 years ago by • 0
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7
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3.8k
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DiffBind: dealing with replicates
diffbind chipseq
updated 5.8 years ago by ★ 5.2k • written 5.9 years ago by • 0
1
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1
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885
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DiffBind t-statistic values
r DiffBind ATAC
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by • 0
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1
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1.3k
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DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by ▴ 10
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3
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2.3k
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Change color of Diffbind's PCA and clustered heatmap plot()
DiffBind plot color
updated 6.0 years ago by ★ 5.2k • written 6.2 years ago by ▴ 10
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1
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675
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DiffBind PCA plot is not showing all samples from sample sheet
DiffBind
updated 6.0 years ago by ★ 5.2k • written 6.0 years ago by ▴ 10
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1
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942
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DiffBind plot size and labels
Diffbind
updated 6.0 years ago by ★ 5.2k • written 6.0 years ago by ▴ 10
0
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2
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815
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How to control the text size for colAttributes in the annotation bar for dbaplot() or dba.plotHeatmap()
diffbind dbaplot() dba.plotHeatmap()
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
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829
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How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
6.2 years ago • updated 6.1 years ago researcher • 0
0
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2
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893
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Diffbind GLM Design
diffbind
updated 6.2 years ago by ★ 5.2k • written 6.2 years ago by • 0
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8
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1.8k
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Question on bgzf_read error
diffbind
6.2 years ago Kath • 0
1
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1
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941
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diffBind volcano plot error
DiffBind volcano plot software error
6.2 years ago rbronste ▴ 60
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4
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1.2k
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DiffBind block not working for me
diffbind
updated 6.2 years ago by ★ 5.2k • written 6.2 years ago by • 0
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2
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2.7k
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DiffBind without replicates
DiffBind
updated 6.2 years ago by ★ 5.2k • written 6.2 years ago by • 0
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3
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2.5k
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DiffBind minOverlap parameter
DiffBind minOverlap consensus peakset Job
updated 4.1 years ago by ★ 5.2k • written 6.2 years ago by • 0
2
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3
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2.2k
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Filtering counts in SummarizedExperiment
diffbind matrix summarizedexperiment rangedCounts
updated 6.2 years ago by ★ 5.2k • written 6.3 years ago by ▴ 60
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4
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in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 6.2 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
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1.0k
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dba.count filter example in manual
diffbind
updated 6.2 years ago by ★ 5.2k • written 6.3 years ago by ▴ 60
1
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1
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1.3k
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 6.2 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
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1
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1.0k
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diffbind counts as same values
diffbind dba.count dba.report
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by • 0
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1
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1.1k
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Help with DiffBind plotVenn and referencing peak sets in general
DiffBind consensus peaks venn
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by • 0
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3
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1.0k
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diffbind plotVenn by Factor
diffbind plotVenn
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
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2
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4.4k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
6.3 years ago researcher • 0
0
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1
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1.4k
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How to find sites with H3K27me3 loss?
Chip Seq Histone H3K27me3 macs diffbind
6.4 years ago researcher • 0
0
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1
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1.9k
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diffBind analysis: only one replicate
diffbind chipseq
updated 2.7 years ago by • 0 • written 6.4 years ago by • 0
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1
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1.2k
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Can we change the name of the ColAttributes in the image generated by dba.plotHeatmap?
DiffBind plot plotHeatmap dba.plotHeatmap
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
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2
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1.5k
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Can we control colors for two different colAtributes
diffbind plot plotHeatmap
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
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1
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1.9k
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DiffBind dba error
DiffBind dba R error
updated 6.4 years ago by ★ 5.2k • written 6.6 years ago by • 0
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2
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1.7k
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DiffBind dba.count error pv$merge(bed): attempt to apply non-function
DiffBind
updated 6.4 years ago by ★ 5.2k • written 6.6 years ago by • 0
0
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4
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1.8k
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diffbind dba.plotvolcano bLabels option use genames instead of numbers
diffbind
updated 6.4 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
0
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2
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846
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How can we increase the width of the correlation plot generated by DiffBind
DiffBind plot(DBdata)
updated 6.4 years ago by ★ 5.2k • written 6.5 years ago by • 0
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3
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2.3k
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diffbind dba object subset peak regions
diffbind
updated 6.4 years ago by ★ 5.2k • written 6.5 years ago by ▴ 160
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1
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1.1k
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Diffbind problems with negative widths in IRanges and chromosome ranges after dba.report
diffbind IRanges
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
0
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5
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4.6k
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How can I remove the row and column labels/names in the plot() or dba.plotHeatmap() while plotting correlation matrix using diffbind?
Diffbind plot heatmap.3
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
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3
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1.4k
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Diffbind batch effect blocking error
Diffbind ATAC batch correction blocking factor
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
4
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5
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1.7k
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diffBind: differentially bound sites are highly different between using EDGER and DESEQ2
diffbind
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
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3
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1.4k
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diffbind change conditions dinamically
diffbind conditions edit
6.5 years ago inzirio ▴ 10
2
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1
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1.3k
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> DBdata <-dba(sampleSheet = samples) Error: object of type 'closure' is not subsettable
DiffBind R R Studio
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
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895
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Error in DBA_OLAP_RATE
diffbind
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by • 0
0
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1
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576
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Package for RNA-Chromatin Interaction Matrix for Differential Gene Feature Calling?
Differential Peak Calling DiffBind DESeq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
1
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2
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1.6k
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DiffBind returns empty consensus peakset
DiffBind consensus
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by • 0
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2
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4.5k
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Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 17 months ago by ▴ 20 • written 6.6 years ago by • 0
2
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2
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3.8k
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DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
2
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1
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1.6k
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DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
diffbind
6.6 years ago melnuesch ▴ 10
0
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3
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1.4k
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Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by • 0
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4
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2.8k
views
Diffbind: Using bigwig tracks in place of bam files
diffbind
updated 6.8 years ago by ▴ 670 • written 6.8 years ago by • 0
3
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4
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2.9k
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Can I input peak files from Genrich as input reads in DiffBind?
DiffBind Genrich
updated 6.8 years ago by ★ 5.2k • written 6.8 years ago by • 0
2
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1
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2.0k
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Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.8 years ago by ★ 5.2k • written 6.8 years ago by ▴ 10
679 results • Page 7 of 14
Recent ...
Replies
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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