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Views
Votes
Showing :
DiffBind
•
reset
2
votes
6
replies
143
views
Interpret plot from DiffBind
DiffBind
7 days ago • updated 1 hour ago
Chris
• 0
0
votes
0
replies
23
views
Title in dba.plotProfile
DiffBind
2 days ago
agata17
• 0
0
votes
1
reply
97
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 8 days ago by
Rory Stark
★ 4.9k • written 15 days ago by
littlefishes20
▴ 10
0
votes
1
reply
140
views
DiffBind dba() in parallel
DiffBind
updated 8 days ago by
Rory Stark
★ 4.9k • written 9 days ago by
Shashank
• 0
1
vote
4
replies
219
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 12 hours ago by
Rory Stark
★ 4.9k • written 9 days ago by
lin.pei26
• 0
0
votes
0
replies
48
views
Fold values in Diffbind
DiffBind
9 days ago
bhandary.8590
• 0
0
votes
3
replies
167
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 10 days ago by
jandrade
• 0
0
votes
0
replies
99
views
Help with Diffbind result
DiffBind
17 days ago
Chris
• 0
3
votes
4
replies
277
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
24 days ago
Mark
• 0
0
votes
7
replies
445
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
6 weeks ago • updated 2 days ago
Ti
• 0
2
votes
1
reply
151
views
how diffbind count the reads of each peak in each sample?
diffbind
DiffBind
updated 6 weeks ago by
Rory Stark
★ 4.9k • written 6 weeks ago by
hfyuan2016
• 0
0
votes
5
replies
337
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 25 days ago by
householdelsewhere
• 0 • written 6 weeks ago by
Oscar
• 0
3
votes
6
replies
283
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
6 weeks ago
Chris
• 0
0
votes
1
reply
179
views
Plotting read densities from DiffBind results
Read
density
DiffBind
updated 7 weeks ago by
Rory Stark
★ 4.9k • written 8 weeks ago by
bhandary.8590
• 0
0
votes
2
replies
183
views
Question regarding multiple comparisons in DiffBind
DiffBind
8 weeks ago • updated 6 weeks ago
epipally
• 0
7
votes
13
replies
724
views
Help with Error in DiffBind
DiffBind
ATACSeq
10 weeks ago • updated 8 weeks ago
Chris
• 0
0
votes
2
replies
224
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 9 weeks ago by
Rory Stark
★ 4.9k • written 9 weeks ago by
os306
• 0
0
votes
2
replies
272
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
10 weeks ago
Giulia
• 0
0
votes
0
replies
96
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
10 weeks ago
Giulia
• 0
1
vote
3
replies
178
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 11 weeks ago by
Rory Stark
★ 4.9k • written 11 weeks ago by
ssankar3
• 0
1
vote
2
replies
174
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
12 weeks ago • updated 11 weeks ago
Weisheng
• 0
0
votes
13
replies
542
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze
DiffBind
@rory-stark-5741
11 weeks ago • updated 9 weeks ago
tahir.msajid
• 0
0
votes
1
reply
132
views
DiffBind---peak region reads or all reads?
DiffBind
updated 11 weeks ago by
Rory Stark
★ 4.9k • written 3 months ago by
skyyks123
• 0
0
votes
0
replies
86
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind
MeRIP-seq
m6A-seq
12 weeks ago
zhiyi
• 0
0
votes
1
reply
200
views
DiffBind differential analysis
DifferentialPeakCalling
ChIPanalyser
DiffBind
chipseqDB
updated 3 months ago by
Rory Stark
★ 4.9k • written 3 months ago by
narzouni
• 0
1
vote
3
replies
358
views
DiffBind---Normalization problem-spike in or no spike in beforehand?
DiffBind
updated 3 months ago by
Rory Stark
★ 4.9k • written 3 months ago by
skyyks123
• 0
0
votes
1
reply
182
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 3 months ago by
Rory Stark
★ 4.9k • written 4 months ago by
Hadar
• 0
0
votes
1
reply
186
views
Setting DBA$config$mergeOverlap for Diffbind
DiffBind
updated 3 months ago by
Rory Stark
★ 4.9k • written 3 months ago by
slrpatty
• 0
0
votes
2
replies
255
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 4 months ago by
Rory Stark
★ 4.9k • written 4 months ago by
slrpatty
• 0
0
votes
7
replies
504
views
Issue in generating a new DBA object with custom counts
DiffBind
dbaobject
5 months ago • updated 4 months ago
francesco.gandolfi
• 0
0
votes
1
reply
245
views
Diffbind matrix/batch effect/normalization
DiffBind
updated 4 months ago by
Rory Stark
★ 4.9k • written 6 months ago by
littlefishes20
▴ 10
0
votes
8
replies
454
views
Question about Diffbind counts
DiffBind
4 months ago
slrpatty
• 0
0
votes
3
replies
402
views
Minor issue regarding customization of text size in Volcano and Heatmap Plots
DiffBind
updated 4 months ago by
Rory Stark
★ 4.9k • written 5 months ago by
cesar.arenasmena
▴ 10
0
votes
1
reply
190
views
dba.count Error in DiffBind
DiffBind
4 months ago
narzouni
• 0
3
votes
4
replies
580
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
5 months ago • updated 4 months ago
spg
• 0
0
votes
1
reply
366
views
DiffBind: Error in pv$called[, mask] : subscript out of bounds
DiffBind
updated 5 months ago by
Rory Stark
★ 4.9k • written 6 months ago by
Pablo
• 0
1
vote
2
replies
246
views
DiffBind Loss and Gain location
DiffBind
updated 4 months ago by
Rory Stark
★ 4.9k • written 5 months ago by
Junsik
• 0
0
votes
2
replies
351
views
Blacklist error in DiffBind
DiffBind
Blacklist
6 months ago
Romain
• 0
2
votes
1
reply
342
views
Error in DiffBind dba.blacklist & dba.count
DiffBind
updated 6 months ago by
Rory Stark
★ 4.9k • written 6 months ago by
Stevie Pederson
• 0
2
votes
1
reply
316
views
Different sequencing depth between replicates and samples
DESeq2
edgeR
DiffBind
updated 7 months ago by
Gordon Smyth
47k • written 7 months ago by
cesar.arenasmena
▴ 10
2
votes
12
replies
899
views
Too much data for Diffbind
DiffBind
7 months ago
littlefishes20
▴ 10
2
votes
4
replies
503
views
DiffBind and peak counts as input
DESeq2
edgeR
DiffBind
updated 6 months ago by
Rory Stark
★ 4.9k • written 7 months ago by
Bogdan
▴ 660
1
vote
25
replies
1.6k
views
DiffBind spike-in normalization
DiffBind
7 months ago
yuhuihui2011
• 0
0
votes
1
reply
389
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq
DiffBind
updated 7 months ago by
Rory Stark
★ 4.9k • written 7 months ago by
Nicole
• 0
2
votes
4
replies
824
views
Normalizing Cut&Tag peak data
Normalization
Peakdata
DiffBind
Cut&Tag
updated 7 months ago by
ATpoint
★ 2.9k • written 8 months ago by
bhandary.8590
• 0
0
votes
3
replies
394
views
Issue carrying out DiffBind Analysis at a predefined peak set
DiffBind
updated 7 months ago by
Rory Stark
★ 4.9k • written 8 months ago by
doherta6
• 0
2
votes
1
reply
934
views
DiffBind: Error in if (res$config$bCorPlot) { : the condition has length > 1
DiffBind
ChIPQC
updated 8 months ago by
Rory Stark
★ 4.9k • written 9 months ago by
ryleehackley
• 0
0
votes
7
replies
1.1k
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 9 months ago by
arisarkar88
▴ 40 • written 3.1 years ago by
bioinfouser2
▴ 10
1
vote
2
replies
444
views
Could it be possible to get an older version of ChIPQC?
ChIPQC
ChIP-seq
DiffBind
Rory_Stark
10 months ago
etiennedanis
• 0
0
votes
2
replies
552
views
DESeq2 analysis has not been run for this contrast
R
DiffBind
10 months ago
Wang
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Gordon Smyth
47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind
by
Chris
• 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind
by
Chris
• 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting
by
phelankj
• 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting
by
James W. MacDonald
63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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