Showing : Diffbind • reset
1
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16
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3.6k
views
Error: could not find function "dba"
software error diffbind dba
7.5 years ago • updated 7.4 years ago mmarins • 0
0
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14
replies
2.4k
views
got 0 significant differential bound (DB)
diffbind
6.9 years ago • updated 6.8 years ago mforoo1 • 0
0
votes
7
replies
1.9k
views
DiffBind:Treatments + second factor
DiffBind diffbind
updated 9.4 years ago by ★ 5.1k • written 9.4 years ago by • 0
16
votes
9
replies
6.5k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 6.5 years ago by ★ 5.1k • written 8.1 years ago by ▴ 60
3
votes
6
replies
4.4k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
6.4 years ago Hesh ▴ 10
0
votes
9
replies
2.7k
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
3.4 years ago • updated 2.2 years ago Tongjun • 0
0
votes
6
replies
1.5k
views
DiffBind error with dba.count
diffbind
updated 6.0 years ago by ★ 5.1k • written 6.0 years ago by • 0
6
votes
8
replies
2.4k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 3.3 years ago by • 0 • written 6.5 years ago by ▴ 60
1
vote
6
replies
5.8k
views
question about DiffBind
DiffBind differential binding analysis
updated 8.6 years ago by ★ 5.1k • written 8.7 years ago by • 0
3
votes
5
replies
2.5k
views
Work with GRanges objects in DiffBind
diffbind
updated 7.7 years ago by ▴ 10 • written 8.7 years ago by • 0
1
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6
replies
2.5k
views
Diffbind EdgeR and DESeq2 normalization
diffbind normalized counts
7.8 years ago GFM ▴ 20
2
votes
6
replies
2.2k
views
SICER and Diffbind
Sicer diffbind
9.1 years ago • updated 9.0 years ago sergio.espeso-gil • 0
0
votes
4
replies
1.4k
views
DiffBind: Report differential sites by fold > & < 0
diffbind
updated 9.4 years ago by ★ 5.1k • written 9.4 years ago by • 0
2
votes
4
replies
824
views
Extracting origin info from DB sites
DiffBind
updated 6.2 years ago by ★ 5.1k • written 6.2 years ago by • 0
0
votes
6
replies
2.9k
views
DiffBind: Error in heights * sapply(called, function(x) x)
diffbind dba.count summits
updated 3.2 years ago by ★ 5.1k • written 6.4 years ago by • 0
2
votes
7
replies
1.3k
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 3.8 years ago by ★ 5.1k • written 3.8 years ago by ▴ 20
3
votes
11
replies
3.2k
views
How to get all possible comparisons in DiffBind
diffbind
updated 2.2 years ago by ★ 5.1k • written 5.3 years ago by • 0
0
votes
4
replies
2.6k
views
Diffbind - Problem with calling plotting functions after analysis "contrasts greater than the number of contrasts"
Diffbind
9.5 years ago ben • 0
1
vote
4
replies
1.3k
views
DiifBind version difference
diffbind new version
updated 8.9 years ago by ★ 5.1k • written 8.9 years ago by • 0
0
votes
4
replies
1.8k
views
How to set the parameter "fragmentSize" in DiffBind and set parameter for paired-end CHIP-seq data?
diffbind software error
updated 6.7 years ago by ★ 5.1k • written 6.7 years ago by • 0
1
vote
4
replies
1.9k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 3.4 years ago by ★ 5.1k • written 6.2 years ago by • 0
0
votes
4
replies
1.6k
views
consensus analysis and dba.count function
diffbind consensus
7.3 years ago • updated 7.2 years ago pabla86 • 0
1
vote
5
replies
4.7k
views
DiffBind error
Alignment DiffBind Alignment DiffBind
updated 11.2 years ago by ★ 5.1k • written 11.2 years ago by ▴ 280
0
votes
4
replies
2.3k
views
Error with Diffbind
diffbind
updated 8.6 years ago by ★ 5.1k • written 8.6 years ago by • 0
2
votes
4
replies
2.0k
views
Normalizing Cut&Tag peak data
Normalization Peakdata DiffBind Cut&amp;Tag
updated 18 months ago by ★ 4.0k • written 18 months ago by ▴ 20
4
votes
8
replies
2.2k
views
ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind ChIPQC
8.2 years ago JD ▴ 10
0
votes
8
replies
4.5k
views
DiffBind - Error in dba.count() when passing mask or peaks
diffbind
updated 8.0 years ago by • 0 • written 8.1 years ago by • 0
1
vote
7
replies
1.4k
views
Conc_1 in differnet dba.report result is slightly different
DiffBind
updated 3.2 years ago by ★ 5.1k • written 3.3 years ago by ▴ 40
0
votes
7
replies
1.1k
views
Issue in generating a new DBA object with custom counts
DiffBind dbaobject
16 months ago • updated 15 months ago francesco.gandolfi • 0
0
votes
5
replies
1.5k
views
Change DiffBind correlation matrix scale
diffbind scale correlation matrix
8.4 years ago eli7javasky • 0
5
votes
7
replies
3.5k
views
What does dba.PCA in DiffBind exactly do?
diffbind pca
updated 2.7 years ago by ★ 5.1k • written 8.5 years ago by ▴ 20
0
votes
5
replies
2.0k
views
error loading dba in DiffBind
DiffBind DiffBind
updated 10.8 years ago by ▴ 30 • written 10.8 years ago by ▴ 650
5
votes
10
replies
1.8k
views
Learning DiffBind - some basic questions
DiffBind
updated 3.1 years ago by ★ 5.1k • written 3.3 years ago by ▴ 10
3
votes
4
replies
2.4k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 2.5 years ago by ▴ 10 • written 5.7 years ago by ▴ 10
2
votes
6
replies
4.1k
views
DiffBind installation doesn't work
diffbind go.db
8.9 years ago • updated 8.8 years ago Gary ▴ 20
0
votes
6
replies
1.4k
views
Unexpected results in the dba.report output files
diffbind
updated 6.3 years ago by • 0 • written 6.5 years ago by • 0
0
votes
4
replies
1.1k
views
Plotting the peak counts for filtering
diffbind
updated 8.9 years ago by ★ 5.1k • written 8.9 years ago by • 0
1
vote
4
replies
2.1k
views
DiffBind not accessible files in Example data
diffbind
updated 2.9 years ago by ★ 5.1k • written 6.4 years ago by • 0
3
votes
12
replies
3.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.7 years ago by ★ 5.1k • written 4.6 years ago by ▴ 20
1
vote
16
replies
4.8k
views
DiffBind Batch Effect
diffbind atac
6.9 years ago niu.shengyong • 0
5
votes
17
replies
1.8k
views
DiffBind : More fragment sizes than libraries
diffbind
updated 6.8 years ago by ★ 5.1k • written 6.8 years ago by ▴ 40
4
votes
7
replies
2.5k
views
Diffbind dba.analyze Error in d$span : $ operator is invalid for atomic vectors
diffbind
updated 13 months ago by • 0 • written 9.1 years ago by ▴ 10
0
votes
5
replies
1.8k
views
ChIPseq diffbind merging peaks
diffbind merging_peaks
7.2 years ago • updated 7.1 years ago veronique.storme • 0
1
vote
8
replies
1.9k
views
Global reduction of epigenetic factors (regularized log transformation DESeq2) ~ Diffbind
deseq2 diffbind
updated 6.9 years ago by 41k • written 6.9 years ago by ▴ 40
2
votes
6
replies
3.4k
views
DiffBind: reading in peaksets generated by Homer2
diffbind
updated 9.0 years ago by • 0 • written 9.3 years ago by ▴ 10
0
votes
3
replies
1.4k
views
DiffBind EdgeR vs DeSeq2 diff peak counts
diffbind
7.3 years ago • updated 7.2 years ago rbronste ▴ 60
4
votes
5
replies
1.8k
views
Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 6.5 years ago by ▴ 30
0
votes
3
replies
1.5k
views
Change color of Diffbind's PCA and clustered heatmap plot()
DiffBind plot color
updated 4.2 years ago by ★ 5.1k • written 4.4 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Diffbind: overlapping + Venn diagram
diffbind
9.4 years ago • updated 9.3 years ago sergio.espeso-gil • 0
0
votes
7
replies
1.7k
views
DiffBind fails to derive consensus peaksets
software error chipseq diffbind
updated 9.0 years ago by ▴ 650 • written 9.0 years ago by ▴ 320
50 results • Page 1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it always helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR? Are you starting with…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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