Showing : diffBind • reset
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16
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ATACseq merge peaks
DiffBind
18 hours ago Shloka • 0
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4
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194
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 5 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
2
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2
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145
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[DiffBind] Obtaining normalization factors
DiffBind
12 days ago • updated 9 days ago Henry ▴ 10
2
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2
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352
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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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0
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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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96
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
26 days ago Ankit ▴ 20
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83
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
28 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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228
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago Sam ▴ 10
0
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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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1
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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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231
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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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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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0
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157
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Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
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0
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223
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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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241
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
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1
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917
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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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2
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334
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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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317
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Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
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1
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340
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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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320
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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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389
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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
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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453
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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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433
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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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838
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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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614
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diffbind analyze for wheat
DiffBind
updated 8 weeks ago by • 0 • written 7 months ago by • 0
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
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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456
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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797
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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
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
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1
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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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608
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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
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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
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4
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833
views
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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665
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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
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1
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534
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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751
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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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791
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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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418
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
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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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400
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Title in dba.plotProfile
DiffBind
10 months ago agata17 • 0
0
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1
reply
551
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
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647
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.2k • 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 ★ 5.2k • written 11 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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