Showing : diffbind • reset
3
votes
4
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1.8k
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Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
12 months ago Mark • 0
0
votes
2
replies
354
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
2
votes
3
replies
798
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 11 months ago by • 0
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by • 0 • written 2.8 years ago by ▴ 10
0
votes
2
replies
840
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
0
votes
5
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3.1k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
2
votes
4
replies
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 7 months ago by • 0
0
votes
5
replies
1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by ★ 5.2k • written 4.2 years ago by • 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
0
votes
1
reply
549
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 4 months ago by ★ 5.2k • written 6.6 years ago by • 0
1
vote
7
replies
2.9k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
0
votes
4
replies
2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 3 months ago by ★ 5.2k • written 7.8 years ago by • 0
0
votes
1
reply
1.2k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 12 months ago by • 0 • written 4.7 years ago by • 0
0
votes
5
replies
1.4k
views
DiffBind:all samples have 0 counts for all genes.
DiffBind Genrich
updated 10 months ago by • 0 • written 3.5 years ago by • 0
1
vote
4
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999
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by • 0
2
votes
3
replies
1.1k
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 9 months ago by ★ 5.2k • written 3.1 years ago by ▴ 10
1
vote
1
reply
452
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
3
replies
1.1k
views
Blacklist error in DiffBind
DiffBind Blacklist
updated 8 weeks ago by • 0 • written 18 months ago by • 0
8
votes
13
replies
1.9k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
0
votes
3
replies
634
views
diffbind analyze for wheat
DiffBind
updated 9 weeks ago by • 0 • written 7 months ago by • 0
1
vote
2
replies
780
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
0
votes
2
replies
488
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
2
votes
2
replies
467
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 0
3
votes
7
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863
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
votes
5
replies
1.2k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 12 months ago by • 0 • written 12 months ago by • 0
4
votes
4
replies
817
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
0
votes
1
reply
937
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by • 0 • written 8 months ago by • 0
0
votes
3
replies
634
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
2
votes
2
replies
388
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
24 days ago • updated 23 days ago Henry ▴ 10
1
vote
2
replies
684
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
1
reply
567
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 11 months ago by ★ 5.2k • written 11 months ago by ▴ 10
2
votes
3
replies
616
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
0
votes
7
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1.4k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
12 months ago • updated 11 months ago Ti • 0
1
vote
2
replies
630
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago Junsik • 0
0
votes
1
reply
132
views
ATACseq merge peaks
DiffBind
updated 9 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
1
reply
664
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
1
vote
4
replies
1.0k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
1
vote
4
replies
876
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
1
reply
2.3k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 9 months ago by ▴ 20
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
1
vote
1
reply
102
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
0
votes
2
replies
124
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
4 days ago • updated 3 days ago Ian D. ▴ 70
1
vote
1
reply
357
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
2
votes
2
replies
171
views
[DiffBind] Obtaining normalization factors
DiffBind
23 days ago • updated 19 days ago Henry ▴ 10
0
votes
1
reply
301
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
votes
2
replies
248
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 11 weeks ago by • 0 • written 2.4 years ago by • 0
0
votes
0
replies
98
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
5 weeks ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
169
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
50 results • Page 1 of 1
Recent ...
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Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 with no issues at all. If you're having trouble with Bioc installa…
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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