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Showing :
diffbind
•
reset
3
votes
7
replies
363
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 14 days ago by
Chris
• 0
0
votes
2
replies
177
views
diffbind analyze for wheat
DiffBind
13 days ago
zgyu12
• 0
0
votes
1
reply
195
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
4 weeks ago
Mark
• 0
0
votes
0
replies
133
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
4 weeks ago
Mark
• 0
1
vote
2
replies
204
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
7 weeks ago • updated 4 weeks ago
Junsik
• 0
0
votes
2
replies
165
views
DiffBind error
DiffBind
updated 4 weeks ago by
Rory Stark
★ 5.0k • written 6 weeks ago by
M.Vukic
• 0
0
votes
2
replies
305
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 8 weeks ago by
Malcolm Cook
★ 1.6k • written 9 weeks ago by
Nebat
• 0
1
vote
1
reply
447
views
Help with error DiffBind
DiffBind
updated 8 weeks ago by
Rory Stark
★ 5.0k • written 12 weeks ago by
Chris
• 0
0
votes
1
reply
422
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 weeks ago by
Rory Stark
★ 5.0k • written 10 weeks ago by
bhandary.8590
• 0
0
votes
5
replies
415
views
diffbind
DiffBind
chipseq
updated 9 weeks ago by
Rory Stark
★ 5.0k • written 9 weeks ago by
ANAMIKA
• 0
0
votes
3
replies
248
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 9 weeks ago by
Rory Stark
★ 5.0k • written 9 weeks ago by
jason.kost
• 0
0
votes
4
replies
625
views
DiffBind handling of replicates and consensus
diffbind
updated 5 weeks ago by
紫枫
• 0 • written 3.6 years ago by
Jim
• 0
0
votes
4
replies
360
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 weeks ago
Theo
• 0
1
vote
2
replies
344
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 11 weeks ago by
Rory Stark
★ 5.0k • written 11 weeks ago by
Stevie Pederson
• 0
0
votes
1
reply
224
views
DiffBind output issues
DiffBind
updated 3 months ago by
Rory Stark
★ 5.0k • written 3 months ago by
David.Atkinson2
• 0
1
vote
2
replies
328
views
Interpret plots from DiffBind
DiffBind
3 months ago
Chris
• 0
2
votes
2
replies
264
views
Sample sheet file for DiffBind
DiffBind
updated 11 weeks ago by
steffies127
• 0 • written 3 months ago by
Chris
• 0
4
votes
4
replies
365
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
3 months ago
bhandary.8590
• 0
0
votes
0
replies
188
views
Help with error running DiffBind
DiffBind
3 months ago
Chris
• 0
1
vote
5
replies
541
views
Diffbind "No genome detected"
DiffBind
3 months ago
kyliecode
• 0
7
votes
13
replies
918
views
Interpret plot from DiffBind
DiffBind
updated 3 months ago by
Rory Stark
★ 5.0k • written 4 months ago by
Chris
• 0
0
votes
0
replies
168
views
Title in dba.plotProfile
DiffBind
3 months ago
agata17
• 0
0
votes
1
reply
283
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 4 months ago by
Rory Stark
★ 5.0k • written 4 months ago by
littlefishes20
▴ 10
0
votes
1
reply
306
views
DiffBind dba() in parallel
DiffBind
updated 4 months ago by
Rory Stark
★ 5.0k • written 4 months ago by
Shashank
• 0
1
vote
4
replies
473
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 3 months ago by
Rory Stark
★ 5.0k • written 4 months ago by
lin.pei26
• 0
0
votes
0
replies
191
views
Fold values in Diffbind
DiffBind
4 months ago
bhandary.8590
• 0
0
votes
3
replies
418
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 4 months ago by
jandrade
• 0
0
votes
0
replies
231
views
Help with Diffbind result
DiffBind
4 months ago
Chris
• 0
3
votes
4
replies
782
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
4 months ago
Mark
• 0
0
votes
7
replies
775
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
5 months ago • updated 3 months ago
Ti
• 0
2
votes
1
reply
275
views
how diffbind count the reads of each peak in each sample?
diffbind
DiffBind
updated 5 months ago by
Rory Stark
★ 5.0k • written 5 months ago by
hfyuan2016
• 0
0
votes
5
replies
613
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 4 months ago by
householdelsewhere
• 0 • written 5 months ago by
Oscar
• 0
4
votes
6
replies
563
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
5 months ago
Chris
• 0
0
votes
1
reply
293
views
Plotting read densities from DiffBind results
Read
density
DiffBind
updated 5 months ago by
Rory Stark
★ 5.0k • written 5 months ago by
bhandary.8590
• 0
0
votes
2
replies
390
views
Question regarding multiple comparisons in DiffBind
DiffBind
5 months ago
epipally
• 0
8
votes
13
replies
1.4k
views
Help with Error in DiffBind
DiffBind
ATACSeq
6 months ago • updated 5 months ago
Chris
• 0
0
votes
2
replies
452
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 6 months ago by
Rory Stark
★ 5.0k • written 6 months ago by
os306
• 0
0
votes
2
replies
525
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
6 months ago
Giulia
• 0
0
votes
0
replies
215
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
6 months ago
Giulia
• 0
1
vote
3
replies
338
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 6 months ago by
Rory Stark
★ 5.0k • written 6 months ago by
ssankar3
• 0
1
vote
2
replies
307
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
6 months ago
Weisheng
• 0
0
votes
13
replies
853
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze
DiffBind
@rory-stark-5741
6 months ago
tahir.msajid
• 0
0
votes
1
reply
263
views
DiffBind---peak region reads or all reads?
DiffBind
updated 6 months ago by
Rory Stark
★ 5.0k • written 7 months ago by
skyyks123
• 0
0
votes
0
replies
194
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind
MeRIP-seq
m6A-seq
6 months ago
zhiyi
• 0
0
votes
1
reply
412
views
DiffBind differential analysis
DifferentialPeakCalling
ChIPanalyser
DiffBind
chipseqDB
updated 7 months ago by
Rory Stark
★ 5.0k • written 7 months ago by
narzouni
• 0
1
vote
3
replies
545
views
DiffBind---Normalization problem-spike in or no spike in beforehand?
DiffBind
updated 6 months ago by
Rory Stark
★ 5.0k • written 7 months ago by
skyyks123
• 0
0
votes
1
reply
345
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 7 months ago by
Rory Stark
★ 5.0k • written 7 months ago by
Hadar
• 0
0
votes
1
reply
329
views
Setting DBA$config$mergeOverlap for Diffbind
DiffBind
updated 7 months ago by
Rory Stark
★ 5.0k • written 7 months ago by
slrpatty
• 0
0
votes
2
replies
381
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 8 months ago by
Rory Stark
★ 5.0k • written 8 months ago by
slrpatty
• 0
0
votes
7
replies
746
views
Issue in generating a new DBA object with custom counts
DiffBind
dbaobject
9 months ago • updated 8 months ago
francesco.gandolfi
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Michael Love
40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta
by
Michael Love
40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix
by
ATpoint
★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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