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Diffbind
•
reset
0
votes
2
replies
922
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 23 months ago by
Sam
▴ 10
1
vote
2
replies
765
views
Inconsistent results in DiffBind
DiffBind
23 months ago
Sam
▴ 10
1
vote
2
replies
855
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 9 weeks ago by
littlefishes20
▴ 10 • written 23 months ago by
Miquel
• 0
0
votes
0
replies
983
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
23 months ago
jared.andrews07
▴ 30
0
votes
0
replies
948
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 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 2.1 years ago by
Matt Eldridge
▴ 10 • written 2.1 years ago by
r.murakami
• 0
2
votes
2
replies
885
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
2.1 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 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
lin.pei26
• 0
3
votes
7
replies
1.7k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 2.1 years ago by
Chris
▴ 20
0
votes
3
replies
1.2k
views
diffbind analyze for wheat
DiffBind
updated 20 months ago by
Igor
• 0 • written 2.1 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
2.2 years ago
Mark
▴ 10
1
vote
2
replies
1.2k
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
2.2 years ago
Junsik
• 0
0
votes
2
replies
905
views
DiffBind error
DiffBind
updated 2.2 years ago by
Rory Stark
★ 5.2k • written 2.2 years ago by
MajaVu
• 0
0
votes
2
replies
1.9k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 2.3 years ago by
Malcolm Cook
★ 1.6k • written 2.3 years ago by
Nebat
• 0
1
vote
1
reply
3.9k
views
Help with error DiffBind
DiffBind
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 2.3 years ago by
Chris
▴ 20
1
vote
1
reply
5.1k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 2.3 years ago by
bhandary.8590
▴ 20
0
votes
5
replies
7.4k
views
diffbind
DiffBind
chipseq
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 2.3 years ago by
ANAMIKA
• 0
0
votes
3
replies
1.2k
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 2.3 years ago by
jason.kost
• 0
0
votes
5
replies
2.3k
views
DiffBind handling of replicates and consensus
diffbind
updated 2.1 years ago by
Rory Stark
★ 5.2k • written 5.7 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
2.3 years ago
Theo
▴ 10
1
vote
2
replies
1.1k
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 2.3 years ago by
Stevie Pederson
• 0
0
votes
1
reply
1.0k
views
DiffBind output issues
DiffBind
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.4 years ago by
David.Atkinson2
• 0
1
vote
2
replies
1.5k
views
Interpret plots from DiffBind
DiffBind
2.4 years ago
Chris
▴ 20
2
votes
3
replies
1.3k
views
Sample sheet file for DiffBind
DiffBind
updated 22 months ago by
meghanapple2
• 0 • written 2.4 years ago by
Chris
▴ 20
4
votes
4
replies
1.6k
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
2.4 years ago
bhandary.8590
▴ 20
1
vote
0
replies
674
views
Help with error running DiffBind
DiffBind
2.4 years ago
Chris
▴ 20
1
vote
7
replies
2.4k
views
Diffbind "No genome detected"
DiffBind
updated 23 months ago by
James W. MacDonald
68k • written 2.4 years ago by
kyliecode
• 0
8
votes
13
replies
3.4k
views
Interpret plot from DiffBind
DiffBind
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.4 years ago by
Chris
▴ 20
0
votes
0
replies
645
views
Title in dba.plotProfile
DiffBind
2.4 years ago
agata17
• 0
0
votes
1
reply
886
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.5 years ago by
littlefishes20
▴ 10
0
votes
1
reply
1.2k
views
DiffBind dba() in parallel
DiffBind
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.5 years ago by
Shashank
• 0
1
vote
4
replies
2.2k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.4 years ago by
lin.pei26
• 0
1
vote
0
replies
1.0k
views
Fold values in Diffbind
DiffBind
2.5 years ago
bhandary.8590
▴ 20
2
votes
3
replies
1.2k
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 2.5 years ago by
jandrade
• 0
0
votes
0
replies
784
views
Help with Diffbind result
DiffBind
2.5 years ago
Chris
▴ 20
3
votes
5
replies
4.0k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
updated 3 months ago by
gunkata9454
• 0 • written 2.5 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
2.5 years ago • updated 2.4 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 2.5 years ago by
Rory Stark
★ 5.2k • written 2.5 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
2.5 years ago
Chris
▴ 20
0
votes
1
reply
953
views
Plotting read densities from DiffBind results
Read
density
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
bhandary.8590
▴ 20
0
votes
2
replies
1.1k
views
Question regarding multiple comparisons in DiffBind
DiffBind
2.6 years ago • updated 2.5 years ago
epipally
• 0
8
votes
13
replies
5.4k
views
Help with Error in DiffBind
DiffBind
ATACSeq
2.6 years ago
Chris
▴ 20
0
votes
2
replies
1.4k
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
os306
• 0
0
votes
2
replies
2.0k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.6 years ago
Giulia
• 0
0
votes
0
replies
821
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.6 years ago
Giulia
• 0
1
vote
3
replies
1.1k
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
ssankar3
• 0
1
vote
2
replies
1.0k
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
2.7 years ago • updated 2.6 years ago
Weisheng
• 0
0
votes
13
replies
2.8k
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze
DiffBind
@rory-stark-5741
2.6 years ago
tahir.msajid
• 0
0
votes
1
reply
683
views
DiffBind---peak region reads or all reads?
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.7 years ago by
skyyks123
• 0
0
votes
0
replies
704
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind
MeRIP-seq
m6A-seq
2.7 years ago
zhiyi
• 0
678 results • Page
2 of 14
Recent ...
Replies
Answer: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis
by
Michael Love
43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
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by
igkryycpinmshzugby
• 0
Yes, Option 1 (technical homogenization) reprocessing paired-end samples as single-end using only R1 is the most defensible approach when l…
Answer: Integration: Paired-end vs healthy single-end from a different source
by
James W. MacDonald
68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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