Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Diffbind
•
reset
0
votes
0
replies
36
views
Setting DBA$config$mergeOverlap for Diffbind
DiffBind
3 days ago
slrpatty
• 0
0
votes
0
replies
37
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
7 days ago
Hadar
• 0
0
votes
2
replies
104
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 16 days ago by
Rory Stark
★ 4.6k • written 21 days ago by
slrpatty
• 0
0
votes
7
replies
306
views
Issue in generating a new DBA object with custom counts
DiffBind
dbaobject
7 weeks ago • updated 23 days ago
francesco.gandolfi
• 0
0
votes
1
reply
118
views
Diffbind matrix/batch effect/normalization
DiffBind
updated 29 days ago by
Rory Stark
★ 4.6k • written 11 weeks ago by
littlefishes20
▴ 10
0
votes
8
replies
276
views
Question about Diffbind counts
DiffBind
4 weeks ago • updated 21 days ago
slrpatty
• 0
0
votes
3
replies
246
views
Minor issue regarding customization of text size in Volcano and Heatmap Plots
DiffBind
updated 4 weeks ago by
Rory Stark
★ 4.6k • written 7 weeks ago by
cesar.arenasmena
▴ 10
0
votes
1
reply
89
views
dba.count Error in DiffBind
DiffBind
4 weeks ago
narzouni
• 0
3
votes
4
replies
328
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
8 weeks ago • updated 4 weeks ago
spg
• 0
0
votes
1
reply
212
views
DiffBind: Error in pv$called[, mask] : subscript out of bounds
DiffBind
updated 7 weeks ago by
Rory Stark
★ 4.6k • written 10 weeks ago by
Pablo
• 0
1
vote
2
replies
154
views
DiffBind Loss and Gain location
DiffBind
updated 4 weeks ago by
Rory Stark
★ 4.6k • written 8 weeks ago by
Junsik
• 0
0
votes
2
replies
214
views
Blacklist error in DiffBind
DiffBind
Blacklist
12 weeks ago
Romain
• 0
1
vote
1
reply
172
views
Error in DiffBind dba.blacklist & dba.count
DiffBind
updated 12 weeks ago by
Rory Stark
★ 4.6k • written 12 weeks ago by
Stevie Pederson
• 0
2
votes
1
reply
180
views
Different sequencing depth between replicates and samples
DESeq2
edgeR
DiffBind
updated 3 months ago by
Gordon Smyth
47k • written 3 months ago by
cesar.arenasmena
▴ 10
2
votes
12
replies
604
views
Too much data for Diffbind
DiffBind
3 months ago
littlefishes20
▴ 10
2
votes
4
replies
324
views
DiffBind and peak counts as input
DESeq2
edgeR
DiffBind
updated 9 weeks ago by
Rory Stark
★ 4.6k • written 3 months ago by
Bogdan
▴ 660
1
vote
25
replies
1.1k
views
DiffBind spike-in normalization
DiffBind
3 months ago
yuhuihui2011
• 0
0
votes
1
reply
253
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq
DiffBind
updated 3 months ago by
Rory Stark
★ 4.6k • written 4 months ago by
Nicole
• 0
2
votes
4
replies
520
views
Normalizing Cut&Tag peak data
Normalization
Peakdata
DiffBind
Cut&Tag
updated 4 months ago by
ATpoint
★ 2.1k • written 4 months ago by
bhandary.8590
• 0
0
votes
3
replies
257
views
Issue carrying out DiffBind Analysis at a predefined peak set
DiffBind
updated 4 months ago by
Rory Stark
★ 4.6k • written 4 months ago by
doherta6
• 0
2
votes
1
reply
526
views
DiffBind: Error in if (res$config$bCorPlot) { : the condition has length > 1
DiffBind
ChIPQC
updated 5 months ago by
Rory Stark
★ 4.6k • written 5 months ago by
ryleehackley
• 0
0
votes
7
replies
902
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 6 months ago by
arisarkar88
▴ 10 • written 2.8 years ago by
bioinfouser2
▴ 10
1
vote
2
replies
330
views
Could it be possible to get an older version of ChIPQC?
ChIPQC
ChIP-seq
DiffBind
Rory_Stark
6 months ago
etiennedanis
• 0
0
votes
2
replies
367
views
DESeq2 analysis has not been run for this contrast
R
DiffBind
6 months ago
Wang
• 0
0
votes
1
reply
308
views
DiffBind: dba.plotPCA() ellipse
PrincipalComponent
DiffBind
updated 7 months ago by
swbarnes2
★ 1.2k • written 7 months ago by
Lisa
• 0
1
vote
3
replies
360
views
Low Differentially Bound Sites found with DiffBind
Cut&Run
DiffBind
7 months ago
gannoncottone
• 0
0
votes
1
reply
353
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
updated 7 months ago by
Rory Stark
★ 4.6k • written 7 months ago by
young
• 0
0
votes
1
reply
343
views
During dba(sampleSheet = "samples.csv") step, Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=charac…
DiffBind
updated 7 months ago by
Rory Stark
★ 4.6k • written 7 months ago by
niimabear
• 0
0
votes
1
reply
438
views
DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
DiffBind
updated 7 months ago by
Rory Stark
★ 4.6k • written 7 months ago by
millerh1
▴ 10
0
votes
0
replies
154
views
diffbind dba.report
diffbind
7 months ago
jonathanho1989
• 0
0
votes
0
replies
250
views
diffbind dba.count error
peakfiles
diffbind
HMMRATAC
8 months ago
jonathanho1989
• 0
0
votes
0
replies
203
views
Diffbind not calling sites as differentially bound
DiffBind
8 months ago
ipsc-jl
• 0
0
votes
1
reply
293
views
Diffbind: different results on the same sample depending on contrast parameters
DifferentialExpression
DiffBind
updated 8 months ago by
Rory Stark
★ 4.6k • written 8 months ago by
Luca
• 0
0
votes
0
replies
279
views
How to set $control.subtract to FALSE in DiffBind?
DiffBind
8 months ago
ksong
▴ 10
0
votes
3
replies
383
views
DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change introduced between version 2.14 and 3.4.11
DiffBind
updated 8 months ago by
Rory Stark
★ 4.6k • written 8 months ago by
chrarnold
• 0
2
votes
5
replies
376
views
Diffbind dba$binding slot finding Chr21 for an MM10 dataset
DiffBind
updated 8 months ago by
sagaryevale121
• 0 • written 9 months ago by
Mehmet
• 0
0
votes
3
replies
368
views
DiffBind on static peak set for all samples
ChIPSeq
DiffBind
updated 9 months ago by
Rory Stark
★ 4.6k • written 9 months ago by
Drew
• 0
2
votes
3
replies
396
views
DiffBind always reverts to default normalization
ATACSeq
Normalization
DiffBind
9 months ago • updated 8 months ago
bers.anthrope
• 0
0
votes
1
reply
356
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq
DiffBind
updated 10 months ago by
Rory Stark
★ 4.6k • written 11 months ago by
rita.rebollo
• 0
0
votes
0
replies
255
views
DiffBind does not load samples
DiffBind
10 months ago
nw416
• 0
3
votes
6
replies
1.2k
views
Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind
dba.plotPCA
updated 5 months ago by
aaweiner
• 0 • written 21 months ago by
Spendlove
▴ 10
1
vote
1
reply
381
views
DiffBind drop out some peaks
DiffBind
updated 10 months ago by
Rory Stark
★ 4.6k • written 10 months ago by
soyabean
• 0
0
votes
0
replies
296
views
Creating a consensus peakset in DiffBind for all the conditions of an experiment
DiffBind
10 months ago
Sam
▴ 10
1
vote
2
replies
836
views
BiocParallel error when running DiffBind
BiocParallel
BiocPa
DiffBind
updated 10 months ago by
Martin Morgan
25k • written 11 months ago by
r.finn
▴ 10
0
votes
0
replies
349
views
DiffBind error
DiffBind
DifferentialPeakCalling
11 months ago
Amandeep
• 0
0
votes
1
reply
282
views
DiffBind contrast design - pairwise with independent filtering
DiffBind
updated 9 months ago by
kathi
• 0 • written 11 months ago by
rita.rebollo
• 0
0
votes
9
replies
1.6k
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
2.2 years ago • updated 11 months ago
Tongjun
• 0
5
votes
6
replies
677
views
How to get 3/4 peak overlap in DiffBind?
DiffBind
12 months ago • updated 11 months ago
Krista
• 0
3
votes
11
replies
1.9k
views
How to get all possible comparisons in DiffBind
diffbind
updated 12 months ago by
Rory Stark
★ 4.6k • written 4.1 years ago by
bony.dekumar
• 0
0
votes
7
replies
983
views
dba.count() error when re-centering peaks
DiffBind
updated 6 months ago by
njrobins
• 0 • written 12 months ago by
Mark
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 and heatmap for multiple comparisons
by
artem.vorobyev
• 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets
by
nicklesteele532
• 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions?
by
Hervé Pagès
16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons
by
swbarnes2
★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Awards
• All
Popular Question
to
Chris
• 0
Popular Question
to
Malcolm Cook
★ 1.6k
Popular Question
to
Hervé Pagès
16k
Popular Question
to
Hans-Ulrich Klein
▴ 330
Popular Question
to
JoeMG
• 0
Locations
• All
Israel,
just now
EMBL Heidelberg,
1 minute ago
Netherlands,
6 minutes ago
France,
13 minutes ago
WEHI, Melbourne, Australia,
14 minutes ago
Traffic: 588 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6