Showing : Diffbind • reset
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21
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ATACseq merge peaks
DiffBind
1 day ago Shloka • 0
0
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4
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198
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 days ago • updated 5 days ago lonn • 0
0
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0
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76
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
10 days ago Virangika • 0
2
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2
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147
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[DiffBind] Obtaining normalization factors
DiffBind
13 days ago • updated 9 days ago Henry ▴ 10
2
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2
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354
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
14 days ago • updated 13 days ago Henry ▴ 10
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0
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98
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
27 days ago feather-W • 0
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0
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96
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
27 days ago Ankit ▴ 20
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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
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0
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126
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
5 weeks ago erbrocato • 0
0
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2
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229
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago Sam ▴ 10
0
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1
reply
187
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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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1
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288
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
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0
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232
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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
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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
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159
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Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
0
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0
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225
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
3 months ago Hai • 0
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0
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245
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
0
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1
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919
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DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by • 0 • written 8 months ago by • 0
0
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2
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336
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
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2
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318
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Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
vote
1
reply
342
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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
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321
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
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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
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
2
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2
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455
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 0
1
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1
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437
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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
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7
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841
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
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3
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616
views
diffbind analyze for wheat
DiffBind
updated 8 weeks ago by • 0 • written 7 months ago by • 0
0
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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
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2
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597
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
0
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2
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458
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
0
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2
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801
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
1
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1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 9 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
0
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5
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2.9k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
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3
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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
0
votes
5
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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
4
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837
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
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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
0
votes
1
reply
536
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
1
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2
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753
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
2
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3
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601
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
votes
4
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793
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
0
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0
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419
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
vote
7
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1.2k
views
Diffbind "No genome detected"
DiffBind
updated 4 months ago by 65k • written 10 months ago by • 0
8
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13
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1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
0
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0
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403
views
Title in dba.plotProfile
DiffBind
11 months ago agata17 • 0
0
votes
1
reply
552
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
0
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1
reply
649
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
1
vote
4
replies
997
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
50 results • Page 1 of 1
Recent ...
Replies
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…
Votes
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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