Showing : diffBind • reset
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5
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221
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Diffbind interpretation of data - fold change
DiffBind
13 days ago Vera • 0
0
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0
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210
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
11 weeks ago kim • 0
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0
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157
views
diffbind covariates
DiffBind ATACSeq
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 220
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2
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513
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DiffBind dba.report discrepancy
DiffBind
3 months ago • updated 12 weeks ago aelbassiouny • 0
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0
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120
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DiffBind subset replicates
DiffBind
3 months ago Haiping • 0
0
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0
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202
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
3 months ago Young Boqin • 0
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0
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244
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
4 months ago Alejandro • 0
0
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2
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387
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DiffBind for MBD-seq
MBD-seq DiffBind
4 months ago Marianna ▴ 20
0
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0
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274
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DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
5 months ago Ian D. ▴ 70
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1
reply
312
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DiffBind remove Unplace Chromosome (chrUn)
DiffBind
5 months ago mdidish ▴ 10
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0
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264
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DiffBind dba.plotprofile y-axis range
DiffBind
5 months ago Tara • 0
0
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8
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781
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DiffBind full library size not reliable
DiffBind Reads MACS2 FullLibSize
updated 5 months ago by ★ 5.2k • written 5 months ago by ▴ 20
1
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3
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521
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Create merged ChIP heatmap across conditions
DiffBind profileplyr
updated 6 months ago by ★ 5.2k • written 6 months ago by • 0
0
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0
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404
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
6 months ago gamma.jian ▴ 10
0
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2
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491
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind DifferentialPeakCalling
7 months ago Mallory • 0
0
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0
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277
views
Difference in Contrast in DiffBind
DiffBind
8 months ago user_bioinfo • 0
0
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0
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313
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
8 months ago Dinesh • 0
0
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1
reply
607
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 10 weeks ago by • 0 • written 8 months ago by ▴ 10
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0
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403
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
8 months ago yvonneh • 0
0
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0
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305
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 months ago Ian D. ▴ 70
0
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9
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1.3k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 months ago • updated 3 months ago Ian D. ▴ 70
3
votes
1
reply
534
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 10
0
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1
reply
817
views
ATACseq merge peaks
DiffBind
updated 8 months ago by ★ 4.6k • written 9 months ago by • 0
0
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4
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590
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 months ago lonn • 0
0
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0
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307
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
9 months ago Virangika • 0
2
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2
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663
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[DiffBind] Obtaining normalization factors
DiffBind
9 months ago Henry ▴ 10
2
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2
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1.1k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
9 months ago Henry ▴ 10
0
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0
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398
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
9 months ago feather-W • 0
0
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0
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406
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
9 months ago Ankit ▴ 20
0
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0
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366
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
9 months ago Pierre Lindenbaum ▴ 10
0
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0
replies
396
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
10 months ago erbrocato • 0
0
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2
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645
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
10 months ago Sam ▴ 10
0
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1
reply
489
views
Exact same results in Diffbind with different normalization methods
DiffBind
10 months ago red_bricks ▴ 60
0
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1
reply
653
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
12 months ago isaromero8888 • 0
0
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0
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669
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 months ago Jawahar • 0
0
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0
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389
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
12 months ago frueher • 0
0
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0
replies
366
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
12 months ago Aswathy • 0
0
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0
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535
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
12 months ago Hai • 0
0
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0
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474
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
12 months ago inna.gur • 0
0
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1
reply
1.3k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 12 months ago by • 0 • written 17 months ago by • 0
0
votes
2
replies
666
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 13 months ago by ▴ 10
1
vote
2
replies
576
views
Inconsistent results in DiffBind
DiffBind
13 months ago Sam ▴ 10
1
vote
1
reply
625
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
0
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0
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670
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
14 months ago jared.andrews07 ▴ 30
0
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0
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680
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 15 months ago by 67k • written 15 months ago by • 0
2
votes
4
replies
1.6k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 15 months ago by ▴ 10 • written 15 months ago by • 0
2
votes
2
replies
698
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
15 months ago r.murakami • 0
1
vote
1
reply
809
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 16 months ago by 67k • written 16 months ago by • 0
3
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7
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1.4k
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 16 months ago by ▴ 20
0
votes
3
replies
928
views
diffbind analyze for wheat
DiffBind
updated 10 months ago by • 0 • written 16 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19) by ja.garcia • 0
It has been fixed by the Rbowtie2 maintainers in version 2.12.2. Thank you for the quick fix!
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Amora • 0
You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 750
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
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Answer: SingleCellExperiment convenience function for metadata+expression?
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