Showing : DiffBind • reset
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 8 months ago by • 0 • written 2.8 years ago by ▴ 10
8
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
3
votes
7
replies
847
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
votes
7
replies
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
7
replies
2.9k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.4 years ago by • 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
votes
5
replies
3.0k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months 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 3.4 years 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
0
votes
5
replies
1.1k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 11 months ago by • 0 • written 12 months ago by • 0
1
vote
4
replies
998
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
3
votes
4
replies
1.8k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
11 months ago Mark • 0
4
votes
4
replies
794
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
0
votes
4
replies
1.9k
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
4
replies
200
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 days ago • updated 6 days ago lonn • 0
1
vote
4
replies
843
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
2
votes
4
replies
1.2k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 10 weeks ago by • 0 • written 2.4 years 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 6 months ago by • 0
1
vote
4
replies
985
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by • 0
2
votes
3
replies
602
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • 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
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
0
votes
3
replies
612
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
3
replies
778
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 11 months ago by • 0
0
votes
3
replies
1.1k
views
Blacklist error in DiffBind
DiffBind Blacklist
updated 6 weeks ago by • 0 • written 17 months ago by • 0
0
votes
3
replies
616
views
diffbind analyze for wheat
DiffBind
updated 8 weeks ago by • 0 • written 7 months ago by • 0
2
votes
2
replies
360
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
15 days ago • updated 14 days ago Henry ▴ 10
0
votes
2
replies
230
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago Sam ▴ 10
1
vote
2
replies
601
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
0
votes
2
replies
337
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
vote
2
replies
758
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
0
votes
2
replies
459
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
2
votes
2
replies
150
views
[DiffBind] Obtaining normalization factors
DiffBind
14 days ago • updated 10 days ago Henry ▴ 10
2
votes
2
replies
456
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 0
0
votes
2
replies
804
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
1
vote
2
replies
320
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
vote
2
replies
667
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
votes
1
reply
188
views
Exact same results in Diffbind with different normalization methods
DiffBind
6 weeks ago • updated 5 weeks ago red_bricks ▴ 50
0
votes
1
reply
1.1k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 11 months ago by • 0 • written 4.7 years ago by • 0
1
vote
1
reply
439
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
1
reply
533
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago Mark • 0
0
votes
1
reply
537
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
1
reply
920
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
554
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
1
vote
1
reply
343
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
votes
1
reply
290
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
votes
1
reply
50
views
ATACseq merge peaks
DiffBind
updated 9 hours ago by ★ 4.0k • written 2 days ago by • 0
0
votes
1
reply
651
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
1
vote
1
reply
2.2k
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 9 months ago by • 0
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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