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diffBind
•
reset
0
votes
2
replies
958
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 2.0 years ago by
Sam
▴ 10
1
vote
2
replies
797
views
Inconsistent results in DiffBind
DiffBind
2.0 years ago
Sam
▴ 10
1
vote
2
replies
904
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 3 months ago by
littlefishes20
▴ 10 • written 2.0 years ago by
Miquel
• 0
0
votes
0
replies
1.0k
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
2.1 years ago
jared.andrews07
▴ 30
0
votes
0
replies
975
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
sophie.hfliu
• 0
2
votes
4
replies
1.9k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 2.2 years ago by
Matt Eldridge
▴ 10 • written 2.2 years ago by
r.murakami
• 0
2
votes
2
replies
923
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
2.2 years ago
r.murakami
• 0
1
vote
1
reply
1.2k
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
lin.pei26
• 0
3
votes
7
replies
1.8k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 2.3 years ago by
Chris
▴ 20
0
votes
3
replies
1.2k
views
diffbind analyze for wheat
DiffBind
updated 22 months ago by
Igor
• 0 • written 2.3 years ago by
zgyu12
• 0
0
votes
1
reply
1.1k
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
2.3 years ago
Mark
▴ 10
1
vote
2
replies
1.3k
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
2.4 years ago • updated 2.3 years ago
Junsik
• 0
0
votes
2
replies
928
views
DiffBind error
DiffBind
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 2.3 years ago by
MajaVu
• 0
0
votes
2
replies
2.0k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 2.4 years ago by
Malcolm Cook
★ 1.6k • written 2.4 years ago by
Nebat
• 0
1
vote
1
reply
3.9k
views
Help with error DiffBind
DiffBind
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.5 years ago by
Chris
▴ 20
1
vote
1
reply
5.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.4 years ago by
bhandary.8590
▴ 20
0
votes
5
replies
7.5k
views
diffbind
DiffBind
chipseq
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.4 years ago by
ANAMIKA
• 0
0
votes
3
replies
1.3k
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.4 years ago by
jason.kost
• 0
0
votes
5
replies
2.3k
views
DiffBind handling of replicates and consensus
diffbind
updated 2.2 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
Jim
• 0
1
vote
4
replies
1.7k
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
2.4 years ago
Theo
▴ 10
1
vote
2
replies
1.2k
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 2.5 years ago by
Rory Stark
★ 5.2k • written 2.5 years ago by
Stevie Pederson
• 0
0
votes
1
reply
1.1k
views
DiffBind output issues
DiffBind
updated 2.5 years ago by
Rory Stark
★ 5.2k • written 2.5 years ago by
David.Atkinson2
• 0
1
vote
2
replies
1.5k
views
Interpret plots from DiffBind
DiffBind
2.5 years ago
Chris
▴ 20
2
votes
3
replies
1.4k
views
Sample sheet file for DiffBind
DiffBind
updated 23 months ago by
meghanapple2
• 0 • written 2.5 years ago by
Chris
▴ 20
4
votes
4
replies
1.7k
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
2.5 years ago
bhandary.8590
▴ 20
1
vote
0
replies
686
views
Help with error running DiffBind
DiffBind
2.5 years ago
Chris
▴ 20
1
vote
7
replies
2.4k
views
Diffbind "No genome detected"
DiffBind
updated 2.1 years ago by
James W. MacDonald
68k • written 2.5 years ago by
kyliecode
• 0
8
votes
13
replies
3.5k
views
Interpret plot from DiffBind
DiffBind
updated 2.5 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
Chris
▴ 20
0
votes
0
replies
663
views
Title in dba.plotProfile
DiffBind
2.6 years ago
agata17
• 0
0
votes
1
reply
907
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
littlefishes20
▴ 10
0
votes
1
reply
1.2k
views
DiffBind dba() in parallel
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
Shashank
• 0
1
vote
4
replies
2.3k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
lin.pei26
• 0
1
vote
0
replies
1.0k
views
Fold values in Diffbind
DiffBind
2.6 years ago
bhandary.8590
▴ 20
2
votes
3
replies
1.3k
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 2.6 years ago by
jandrade
• 0
0
votes
0
replies
802
views
Help with Diffbind result
DiffBind
2.6 years ago
Chris
▴ 20
3
votes
5
replies
4.2k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
updated 4 months ago by
gunkata9454
• 0 • written 2.6 years ago by
Mark
▴ 10
0
votes
7
replies
2.3k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
2.7 years ago • updated 2.6 years ago
Ti
• 0
2
votes
1
reply
1.1k
views
how diffbind count the reads of each peak in each sample?
diffbind
DiffBind
updated 2.7 years ago by
Rory Stark
★ 5.2k • written 2.7 years ago by
hfyuan2016
• 0
4
votes
6
replies
1.7k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
2.7 years ago
Chris
▴ 20
0
votes
1
reply
979
views
Plotting read densities from DiffBind results
Read
density
DiffBind
updated 2.7 years ago by
Rory Stark
★ 5.2k • written 2.7 years ago by
bhandary.8590
▴ 20
0
votes
2
replies
1.2k
views
Question regarding multiple comparisons in DiffBind
DiffBind
2.7 years ago
epipally
• 0
8
votes
13
replies
5.5k
views
Help with Error in DiffBind
DiffBind
ATACSeq
2.7 years ago
Chris
▴ 20
0
votes
2
replies
1.5k
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 2.7 years ago by
Rory Stark
★ 5.2k • written 2.7 years ago by
os306
• 0
0
votes
2
replies
2.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.7 years ago
Giulia
• 0
0
votes
0
replies
844
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.7 years ago
Giulia
• 0
1
vote
3
replies
1.2k
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 2.8 years ago by
Rory Stark
★ 5.2k • written 2.8 years ago by
ssankar3
• 0
1
vote
2
replies
1.1k
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
2.8 years ago
Weisheng
• 0
0
votes
13
replies
2.9k
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze
DiffBind
@rory-stark-5741
2.8 years ago • updated 2.7 years ago
tahir.msajid
• 0
0
votes
1
reply
704
views
DiffBind---peak region reads or all reads?
DiffBind
updated 2.8 years ago by
Rory Stark
★ 5.2k • written 2.8 years ago by
skyyks123
• 0
0
votes
0
replies
734
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind
MeRIP-seq
m6A-seq
2.8 years ago
zhiyi
• 0
678 results • Page
2 of 14
Recent ...
Replies
Comment: blockwiseModule crashes in the end and doesn't generate modules
by
gexose2839
• 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA?
by
TikTsokaasocissalpc
• 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
Answer: segfault in edgeR glmQLFit
by
Gordon Smyth
53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. The prob…
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
aqeel
• 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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