Showing : Diffbind • reset
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DiffBind 2.10.0: Consensus peaks seems to miss 2/3 of original sample peaks
DiffBind Consensus peak
updated 5.6 years ago by ★ 5.2k • written 5.7 years ago by • 0
0
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2
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1.1k
views
DiffBind: error with dba.peakset()
DiffBind Peakset
updated 5.6 years ago by ★ 5.2k • written 5.7 years ago by • 0
1
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7
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3.7k
views
DiffBind: dealing with replicates
diffbind chipseq
updated 5.6 years ago by ★ 5.2k • written 5.7 years ago by • 0
1
vote
1
reply
855
views
DiffBind t-statistic values
r DiffBind ATAC
updated 5.7 years ago by ★ 5.2k • written 5.7 years ago by • 0
0
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1
reply
1.2k
views
DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 5.7 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
0
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3
replies
2.2k
views
Change color of Diffbind's PCA and clustered heatmap plot()
DiffBind plot color
updated 5.8 years ago by ★ 5.2k • written 6.0 years ago by ▴ 10
0
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1
reply
628
views
DiffBind PCA plot is not showing all samples from sample sheet
DiffBind
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
0
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1
reply
877
views
DiffBind plot size and labels
Diffbind
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
0
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2
replies
772
views
How to control the text size for colAttributes in the annotation bar for dbaplot() or dba.plotHeatmap()
diffbind dbaplot() dba.plotHeatmap()
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
0
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0
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790
views
How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
6.0 years ago • updated 5.9 years ago researcher • 0
0
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2
replies
853
views
Diffbind GLM Design
diffbind
updated 6.0 years ago by ★ 5.2k • written 6.0 years ago by • 0
0
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8
replies
1.7k
views
Question on bgzf_read error
diffbind
6.0 years ago Kath • 0
1
vote
1
reply
906
views
diffBind volcano plot error
DiffBind volcano plot software error
6.0 years ago rbronste ▴ 60
3
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4
replies
1.2k
views
DiffBind block not working for me
diffbind
updated 6.0 years ago by ★ 5.2k • written 6.0 years ago by • 0
1
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2
replies
2.7k
views
DiffBind without replicates
DiffBind
updated 6.0 years ago by ★ 5.2k • written 6.0 years ago by • 0
0
votes
3
replies
2.4k
views
DiffBind minOverlap parameter
DiffBind minOverlap consensus peakset Job
updated 3.9 years ago by ★ 5.2k • written 6.0 years ago by • 0
2
votes
3
replies
2.1k
views
Filtering counts in SummarizedExperiment
diffbind matrix summarizedexperiment rangedCounts
updated 6.0 years ago by ★ 5.2k • written 6.1 years ago by ▴ 60
1
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4
replies
1.6k
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 6.0 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
0
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1
reply
951
views
dba.count filter example in manual
diffbind
updated 6.0 years ago by ★ 5.2k • written 6.1 years ago by ▴ 60
1
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1
reply
1.2k
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 6.0 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
0
votes
1
reply
954
views
diffbind counts as same values
diffbind dba.count dba.report
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by • 0
0
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1
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1.1k
views
Help with DiffBind plotVenn and referencing peak sets in general
DiffBind consensus peaks venn
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by • 0
0
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3
replies
967
views
diffbind plotVenn by Factor
diffbind plotVenn
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
1
vote
2
replies
4.4k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
6.2 years ago researcher • 0
0
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1
reply
1.3k
views
How to find sites with H3K27me3 loss?
Chip Seq Histone H3K27me3 macs diffbind
6.2 years ago researcher • 0
0
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1
reply
1.8k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 2.5 years ago by • 0 • written 6.2 years ago by • 0
0
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1
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1.2k
views
Can we change the name of the ColAttributes in the image generated by dba.plotHeatmap?
DiffBind plot plotHeatmap dba.plotHeatmap
updated 6.2 years ago by ★ 5.2k • written 6.2 years ago by • 0
0
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2
replies
1.4k
views
Can we control colors for two different colAtributes
diffbind plot plotHeatmap
updated 6.2 years ago by ★ 5.2k • written 6.2 years ago by • 0
0
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1
reply
1.9k
views
DiffBind dba error
DiffBind dba R error
updated 6.2 years ago by ★ 5.2k • written 6.4 years ago by • 0
0
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2
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1.6k
views
DiffBind dba.count error pv$merge(bed): attempt to apply non-function
DiffBind
updated 6.2 years ago by ★ 5.2k • written 6.4 years ago by • 0
0
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4
replies
1.7k
views
diffbind dba.plotvolcano bLabels option use genames instead of numbers
diffbind
updated 6.2 years ago by ★ 5.2k • written 6.4 years ago by ▴ 10
0
votes
2
replies
789
views
How can we increase the width of the correlation plot generated by DiffBind
DiffBind plot(DBdata)
updated 6.2 years ago by ★ 5.2k • written 6.3 years ago by • 0
0
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3
replies
2.2k
views
diffbind dba object subset peak regions
diffbind
updated 6.2 years ago by ★ 5.2k • written 6.3 years ago by ▴ 160
0
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1
reply
1.0k
views
Diffbind problems with negative widths in IRanges and chromosome ranges after dba.report
diffbind IRanges
updated 6.2 years ago by ★ 5.2k • written 6.3 years ago by • 0
0
votes
5
replies
4.5k
views
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 6.2 years ago by ★ 5.2k • written 6.2 years ago by • 0
0
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3
replies
1.4k
views
Diffbind batch effect blocking error
Diffbind ATAC batch correction blocking factor
updated 6.2 years ago by ★ 5.2k • written 6.3 years ago by • 0
4
votes
5
replies
1.7k
views
diffBind: differentially bound sites are highly different between using EDGER and DESEQ2
diffbind
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by • 0
0
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3
replies
1.4k
views
diffbind change conditions dinamically
diffbind conditions edit
6.3 years ago inzirio ▴ 10
2
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1
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1.3k
views
> DBdata <-dba(sampleSheet = samples) Error: object of type 'closure' is not subsettable
DiffBind R R Studio
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 10
0
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1
reply
860
views
Error in DBA_OLAP_RATE
diffbind
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
0
votes
1
reply
552
views
Package for RNA-Chromatin Interaction Matrix for Differential Gene Feature Calling?
Differential Peak Calling DiffBind DESeq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
1
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2
replies
1.5k
views
DiffBind returns empty consensus peakset
DiffBind consensus
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
0
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2
replies
4.3k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 15 months ago by ▴ 20 • written 6.4 years ago by • 0
2
votes
2
replies
3.6k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by ▴ 10
2
votes
1
reply
1.6k
views
DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
diffbind
6.5 years ago melnuesch ▴ 10
0
votes
3
replies
1.3k
views
Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
0
votes
4
replies
2.7k
views
Diffbind: Using bigwig tracks in place of bam files
diffbind
updated 6.6 years ago by ▴ 670 • written 6.6 years ago by • 0
3
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4
replies
2.8k
views
Can I input peak files from Genrich as input reads in DiffBind?
DiffBind Genrich
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by • 0
2
votes
1
reply
2.0k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
0
votes
4
replies
2.8k
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind FRiP ATAC-Seq dba.show dba.count
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by ▴ 20
678 results • Page 7 of 14
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Replies
Comment: Failure to download resources (MeSHDb) from AnnotationHub by Steve Lianoglou ★ 13k
That fixed it, thanks Lori!
Comment: Suppress warning in RHDF5 write by nicolas.lhuillier • 0
Thanks a lot for the quick and effective reply. I had tried "suppressWarnings" but not "suppressMessages".
Answer: Suppress warning in RHDF5 write by James W. MacDonald 68k
``` > fun <- function() message("this is a message") > fun() this is a message > suppressMessages(fun()) > ```
Answer: Failure to download resources (MeSHDb) from AnnotationHub by shepherl 4.2k
apologies. These are contributed by someone outside the core team. On upload I did not realize they included the older Bioconductor storage…
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
Awards • All
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