Showing : DiffBind • reset
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ATACseq merge peaks
DiffBind
3 hours ago • updated 2 hours ago Shloka • 0
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4
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191
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 4 days ago lonn • 0
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76
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
9 days ago Virangika • 0
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2
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143
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[DiffBind] Obtaining normalization factors
DiffBind
12 days ago • updated 8 days ago Henry ▴ 10
2
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351
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
13 days ago • updated 12 days ago Henry ▴ 10
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96
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
26 days ago feather-W • 0
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95
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
26 days ago Ankit ▴ 20
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
27 days ago Pierre Lindenbaum ▴ 10
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125
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
5 weeks ago erbrocato • 0
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2
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227
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago • updated 5 weeks ago Sam ▴ 10
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1
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185
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Exact same results in Diffbind with different normalization methods
DiffBind
6 weeks ago • updated 5 weeks ago red_bricks ▴ 50
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286
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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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229
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
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164
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
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155
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Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
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221
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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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240
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
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916
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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
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333
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
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317
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Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
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1
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339
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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
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319
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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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388
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 6 months ago by 65k • written 6 months ago by • 0
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1.2k
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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
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453
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DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 0
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432
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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 6 months ago by 65k • written 6 months ago by • 0
3
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
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3
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613
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diffbind analyze for wheat
DiffBind
updated 7 weeks ago by • 0 • written 7 months ago by • 0
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1
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531
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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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595
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DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
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2
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454
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DiffBind error
DiffBind
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
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2
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795
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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
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1.9k
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Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
1
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1
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2.2k
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Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.1k • written 9 months ago by ▴ 20
0
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5
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2.9k
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diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
0
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3
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606
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DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
0
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5
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1.1k
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DiffBind handling of replicates and consensus
diffbind
updated 6 months ago by ★ 5.1k • written 4.2 years ago by • 0
1
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4
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831
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diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
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2
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664
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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
0
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1
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534
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DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.1k • written 10 months ago by • 0
1
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2
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749
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Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
2
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3
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599
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Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
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4
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790
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DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
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0
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418
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Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
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7
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1.2k
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Diffbind "No genome detected"
DiffBind
updated 4 months ago by 65k • written 10 months ago by • 0
7
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13
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1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
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0
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400
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Title in dba.plotProfile
DiffBind
10 months ago agata17 • 0
0
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1
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551
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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
0
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1
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646
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.1k • written 11 months ago by • 0
1
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4
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996
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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
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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