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diffBind
•
reset
0
votes
4
replies
2.9k
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind
FRiP
ATAC-Seq
dba.show
dba.count
updated 6.8 years ago by
Rory Stark
★ 5.2k • written 6.8 years ago by
Gary
▴ 20
0
votes
2
replies
2.4k
views
DiffBind peaks input file format
DiffBind
macs2
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 7.0 years ago by
Anna
• 0
0
votes
1
reply
1.7k
views
DiffBind - Counting reads - counts not found
diffbind
differential analysis
genetics
#chip-seq
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 6.9 years ago by
ryclb22
• 0
0
votes
1
reply
975
views
Diffbind plotting options
diffbind
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 6.9 years ago by
Helene
• 0
0
votes
1
reply
2.5k
views
Handing duplicates in DiffBind
diffbind
dba.count
bRemoveDuplicates
bUseSummarizeOverlaps
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 6.9 years ago by
loretta
• 0
1
vote
1
reply
2.0k
views
how to retrieve binding affinity matrix in diffbind
diffbind
dba.count
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 6.9 years ago by
hamaor
• 0
2
votes
2
replies
2.9k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 6.9 years ago by
paz2005
• 0
0
votes
0
replies
776
views
diffbind: use of continuous variables
diffbind
deseq2
7.0 years ago
janani.sundaresan
• 0
2
votes
2
replies
4.9k
views
Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) on using DBA_DESEQ2 with blocking factor.
diffbind
updated 7.0 years ago by
Rory Stark
★ 5.2k • written 7.0 years ago by
avantika6194
• 0
0
votes
0
replies
825
views
DiffBind - Difficulties construction appropriate consensus set
Diffbind
7.1 years ago
Rob Buurstede
• 0
3
votes
7
replies
5.7k
views
DEseq2 for differential binding analysis ChIP seq
deseq2
diffbind
csaw
greylistchip
chipseq
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
Yonatan Amzaleg
• 0
0
votes
0
replies
1.2k
views
Unable to reproduce DiffBind PCA plot
diffbind
news
7.1 years ago
jingyaq
▴ 10
3
votes
5
replies
2.0k
views
News:
sorted the results of function dba.report in DiffBind R package
diffbind
News
updated 7.1 years ago by
Rory Stark
★ 5.2k • written 7.1 years ago by
bioqianyang
• 0
0
votes
0
replies
680
views
Converting DESeq2 results to DiffBind object
deseq2
diffbind
7.2 years ago
rbronste
▴ 60
2
votes
2
replies
2.8k
views
dba.count Can't count: some peaksets are not associated with a .bam file.
diffbind
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
loretta
• 0
3
votes
1
reply
1.0k
views
dba.count binding matrix coordinates
DiffBind
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
jingyaq
▴ 10
0
votes
1
reply
1.8k
views
Use DiffBind to find differential peaks among multiple cell types
diffbind
atac-seq
differential analysis
deseq2
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
duvaller
• 0
1
vote
1
reply
1.2k
views
How to color different column bars independently using dba.plotHeatmap (DiffBind)?
diffbind
dba.plotHeatmap
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
Gary
▴ 20
0
votes
1
reply
1.0k
views
adding a new consensus peakset question
diffbind
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
yuhongning2013
• 0
3
votes
2
replies
2.0k
views
diffbind finding not differential site
diffbind
chipseq
histone chip-seq
differential binding analysis
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
woongjaej
• 0
3
votes
3
replies
1.9k
views
Differential analysis of multiple samples with different time points
diffbind
R
atac-seq
updated 7.3 years ago by
Rory Stark
★ 5.2k • written 7.3 years ago by
Firas
• 0
0
votes
0
replies
1.3k
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind
chip-seq
R
7.3 years ago
pierre.marin
• 0
0
votes
2
replies
1.0k
views
dba.report() output counts
diffbind
updated 7.3 years ago by
Rory Stark
★ 5.2k • written 7.3 years ago by
Shamaine
• 0
0
votes
1
reply
1000
views
Blocking factors for differential binding analysis with DiffBind
diffbind
updated 7.3 years ago by
Rory Stark
★ 5.2k • written 7.6 years ago by
Mthabisi Moyo
▴ 40
2
votes
4
replies
2.0k
views
DiffBind confuses coordinates of peaks
atacseq
diffbind
updated 7.3 years ago by
Rory Stark
★ 5.2k • written 7.3 years ago by
gtechbio
▴ 10
1
vote
3
replies
1.3k
views
How to get peaks summit using dba.peakset
diffbind
updated 7.4 years ago by
Rory Stark
★ 5.2k • written 7.4 years ago by
Udi Landau
▴ 30
1
vote
7
replies
3.8k
views
ChipQC not loading files
ChipQC
diffbind
updated 7.4 years ago by
Thomas Carroll
▴ 420 • written 7.4 years ago by
annap
• 0
1
vote
1
reply
794
views
DESeq2 for ChIP-seq
deseq2
diffbind
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
bioinfo
• 0
0
votes
3
replies
1.3k
views
DiffBind: dba.overlap error
DiffBind
dba.overlap
7.5 years ago
romicakerketta
• 0
1
vote
3
replies
999
views
Question of DiffBind for ChIP-Seq analysis
diffbind
updated 7.5 years ago by
Rory Stark
★ 5.2k • written 7.5 years ago by
mengm5
• 0
5
votes
9
replies
2.7k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2
diffbind
basemean
summarizedexperiment
7.5 years ago
rbronste
▴ 60
2
votes
5
replies
1.9k
views
Differential ChIP-seq analysis
diffbind
csaw
updated 7.5 years ago by
Rory Stark
★ 5.2k • written 7.5 years ago by
bioinfo
• 0
0
votes
1
reply
792
views
DiffBind different read counts depending on dba.count scores specified
DiffBind
7.6 years ago
Lauma R
▴ 10
0
votes
2
replies
2.8k
views
Changing box plot font sizes for axes and labels in DiffBind
diffbind
7.6 years ago
Mthabisi Moyo
▴ 40
1
vote
1
reply
1.0k
views
getting DiffBind full result list
deseq2
diffbind
chipseq
updated 7.6 years ago by
Rory Stark
★ 5.2k • written 7.6 years ago by
rafael.munoz.viana
• 0
0
votes
1
reply
1.1k
views
change x- and y-axis limit within dba.plotVolcano in DiffBind
diffbind
updated 7.6 years ago by
Rory Stark
★ 5.2k • written 7.6 years ago by
Suz
• 0
1
vote
1
reply
946
views
DiffBind question on adb.contrast
diffbind
updated 7.6 years ago by
Rory Stark
★ 5.2k • written 7.6 years ago by
bright602
• 0
2
votes
3
replies
3.7k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind
chipseq
counts
peaks
bedtools
updated 4.7 years ago by
Rory Stark
★ 5.2k • written 7.7 years ago by
Ni-Ar
▴ 10
0
votes
1
reply
1.2k
views
Combine separate dba objects into the one
Diffbind
updated 7.7 years ago by
Rory Stark
★ 5.2k • written 7.7 years ago by
Lauma R
▴ 10
0
votes
0
replies
1.1k
views
Differential ChIP regions across >2 conditions
diffbind
chipseq
7.7 years ago
Shamaine
• 0
1
vote
2
replies
3.6k
views
Diffbind: How do I set up multiple contrasts, for example tissue type and timepoint?
diffbind
updated 7.7 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
estoyanova
• 0
0
votes
6
replies
2.1k
views
DiffBind error with dba.count
diffbind
updated 7.7 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
hhhcce
• 0
3
votes
3
replies
5.4k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind
chipseq
peaks
dba
is.na
7.8 years ago
maria.kondili
▴ 10
0
votes
1
reply
1.0k
views
dba.count generates less ranges than input peakset
diffbind
dba.count
dba.peakset
updated 7.8 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
pau.rodriguez.sodupe
• 0
0
votes
2
replies
1.7k
views
Binding matrix creation DiffBind after MACS2 peak call
diffbind
macs2
updated 7.8 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
Lauma R
▴ 10
0
votes
4
replies
2.6k
views
How to extract overlapping and unique peaks from the Venn Diagram to a csv format in DiffBind?
DiffBind
plotvenn
updated 7.8 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
Hesh
▴ 10
0
votes
4
replies
3.3k
views
DiffBind question: How to extract read counts?
diffbind
read counts
extract data
updated 7.8 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
k.panov
• 0
2
votes
4
replies
1.3k
views
Extracting origin info from DB sites
DiffBind
updated 7.9 years ago by
Rory Stark
★ 5.2k • written 7.9 years ago by
michal.inbar
• 0
1
vote
1
reply
745
views
heatmap of all contrasted sites
DiffBind
updated 7.9 years ago by
Rory Stark
★ 5.2k • written 7.9 years ago by
michal.inbar
• 0
0
votes
1
reply
1.4k
views
DiffBind count warning
diffbind
parallel
updated 7.9 years ago by
Rory Stark
★ 5.2k • written 7.9 years ago by
ghosos
• 0
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