Showing : DiffBind • reset
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21
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ATACseq merge peaks
DiffBind
1 day ago Shloka • 0
0
votes
4
replies
198
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 days ago • updated 5 days ago lonn • 0
2
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2
replies
147
views
[DiffBind] Obtaining normalization factors
DiffBind
13 days ago • updated 9 days ago Henry ▴ 10
0
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0
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76
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
10 days ago Virangika • 0
2
votes
2
replies
354
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
14 days ago • updated 13 days ago Henry ▴ 10
0
votes
0
replies
98
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
27 days ago feather-W • 0
0
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0
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96
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
27 days ago Ankit ▴ 20
0
votes
0
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84
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
28 days ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
126
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
5 weeks ago erbrocato • 0
0
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1
reply
187
views
Exact same results in Diffbind with different normalization methods
DiffBind
6 weeks ago • updated 5 weeks ago red_bricks ▴ 50
0
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2
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229
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago Sam ▴ 10
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
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3
replies
616
views
diffbind analyze for wheat
DiffBind
updated 8 weeks ago by • 0 • written 7 months ago by • 0
2
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4
replies
1.2k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 9 weeks ago by • 0 • written 2.4 years ago by • 0
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
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
0
votes
1
reply
288
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
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0
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232
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
0
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0
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168
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
1
vote
4
replies
983
views
Diffbind error while running example data
DiffBind
written 3.1 years ago by • 0
0
votes
0
replies
159
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
2
votes
3
replies
601
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
0
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0
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225
views
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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245
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
0
votes
1
reply
919
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by • 0 • written 8 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
2
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318
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
0
votes
2
replies
336
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
vote
1
reply
342
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.0k • written 4 months 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
0
replies
321
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
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
2
votes
2
replies
455
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 0
0
votes
0
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392
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
0
votes
5
replies
1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 6 months ago by ★ 5.2k • written 4.2 years ago by • 0
1
vote
1
reply
437
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
3
votes
7
replies
841
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
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
1
vote
2
replies
597
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
0
votes
2
replies
458
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
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
0
votes
2
replies
801
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
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 9 months 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
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
0
votes
5
replies
2.9k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
votes
3
replies
609
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
1
vote
4
replies
837
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
666
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
4
votes
4
replies
793
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
50 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Are you commenting on the OP's question, or adding a different question? If the latter, please start a new post rather than piggybacking on…
Answer: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Use `bquote`. See section 4.6 in [the vignette][1]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/in…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
I was thinking about removing unwanted variations at the sample level (ie a transformation shared across genes) not at the gene level. Corr…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
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biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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