Showing : DiFFBind • reset
0
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4
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134
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
2 days ago • updated 5 hours ago lonn • 0
0
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0
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65
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
4 days ago Virangika • 0
2
votes
2
replies
139
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[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 4 days ago Henry ▴ 10
2
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2
replies
344
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
8 days ago • updated 7 days ago Henry ▴ 10
0
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0
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96
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
21 days ago feather-W • 0
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0
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95
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
22 days ago • updated 21 days ago Ankit ▴ 20
0
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0
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81
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
23 days ago Pierre Lindenbaum ▴ 10
0
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0
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122
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
4 weeks ago erbrocato • 0
0
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2
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219
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
5 weeks ago Sam ▴ 10
0
votes
1
reply
182
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Exact same results in Diffbind with different normalization methods
DiffBind
5 weeks ago • updated 4 weeks ago red_bricks ▴ 50
0
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1
reply
282
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
12 weeks ago isaromero8888 • 0
0
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0
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223
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 weeks ago Jawahar • 0
0
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0
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161
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
0
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0
replies
152
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
0
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0
replies
214
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
3 months ago Hai • 0
0
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0
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235
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
1
vote
2
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314
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
0
votes
2
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329
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
vote
1
reply
334
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
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0
replies
317
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
0
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0
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383
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 6 months ago by 65k • written 6 months ago by • 0
2
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2
replies
450
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 0
2
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4
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1.2k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 6 months ago by • 0 • written 6 months ago by • 0
1
vote
1
reply
428
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 6 months ago by 65k • written 6 months ago by • 0
0
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3
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604
views
diffbind analyze for wheat
DiffBind
updated 7 weeks ago by • 0 • written 7 months ago by • 0
3
votes
7
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834
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
votes
1
reply
528
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
7 months ago Mark • 0
0
votes
1
reply
909
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by • 0 • written 7 months ago by • 0
0
votes
2
replies
445
views
DiffBind error
DiffBind
updated 7 months ago by ★ 5.1k • written 8 months ago by • 0
1
vote
2
replies
591
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago • updated 7 months ago Junsik • 0
0
votes
3
replies
602
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
0
votes
2
replies
786
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 8 months ago by ★ 1.6k • written 8 months ago by • 0
0
votes
5
replies
2.9k
views
diffbind
DiffBind chipseq
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 8 months ago by ★ 5.1k • written 9 months ago by ▴ 20
1
vote
4
replies
815
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
659
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 8 months ago by ★ 5.1k • written 9 months ago by • 0
2
votes
3
replies
594
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
votes
4
replies
787
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago • updated 9 months ago bhandary.8590 ▴ 20
1
vote
2
replies
746
views
Interpret plots from DiffBind
DiffBind
10 months ago • updated 9 months ago Chris • 0
0
votes
1
reply
530
views
DiffBind output issues
DiffBind
updated 9 months ago by ★ 5.1k • written 10 months ago by • 0
0
votes
0
replies
414
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 4 months ago by 65k • written 10 months ago by • 0
0
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0
replies
395
views
Title in dba.plotProfile
DiffBind
10 months ago agata17 • 0
7
votes
13
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1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.1k • written 10 months ago by • 0
1
vote
4
replies
988
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
1
vote
0
replies
544
views
Fold values in Diffbind
DiffBind
11 months ago bhandary.8590 ▴ 20
0
votes
1
reply
643
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.1k • written 11 months ago by • 0
2
votes
3
replies
768
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 11 months ago by • 0
0
votes
1
reply
549
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 11 months ago by ★ 5.1k • written 11 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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