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0
votes
2
replies
254
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 weeks ago • updated 7 weeks ago Sam ▴ 10
0
votes
2
replies
356
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
1
vote
2
replies
332
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
0
votes
5
replies
1.9k
views
How to add a BioConductor package to a Docker image based on rocker/shiny
docker
20 months ago Sam ▴ 10
0
votes
0
replies
606
views
Creating a consensus peakset in DiffBind for all the conditions of an experiment
DiffBind
2.1 years ago Sam ▴ 10
1
vote
2
replies
1.0k
views
What lfcSE is dependent upon?
DESeq2
written 2.8 years ago by ▴ 10
2
votes
1
reply
668
views
Why does samples order subtly influence the results of DESeq2?
DESeq2
updated 2.8 years ago by 42k • written 2.8 years ago by ▴ 10
0
votes
2
replies
723
views
TOAST output
TOAST
3.0 years ago Sam ▴ 10
3
votes
3
replies
788
views
DESeq2 unmix function
DESeq2
updated 3.0 years ago by 42k • written 3.0 years ago by ▴ 10
0
votes
0
replies
841
views
What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.1 years ago Sam ▴ 10
2
votes
3
replies
1.1k
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 9 months ago by ★ 5.2k • written 3.1 years ago by ▴ 10
2
votes
2
replies
1.1k
views
A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 3.1 years ago by ★ 5.2k • written 3.1 years ago by ▴ 10
0
votes
4
replies
982
views
How sensitive is DiffBind to Deseq2 assumptions ?
DESeq2 DiffBind
updated 3.1 years ago by ★ 5.2k • written 3.1 years ago by ▴ 10
1
vote
4
replies
1.7k
views
An attempt to better understand DESeq2 dispersion estimation
DESeq2
3.2 years ago • updated 3.1 years ago Sam ▴ 10
0
votes
3
replies
1.2k
views
Does DiffBind correctly designate peaks with very small fold-change to be statistically significant?
DESeq2 DiffBind
updated 3.0 years ago by ★ 5.2k • written 3.3 years ago by ▴ 10
1
vote
1
reply
697
views
What is the correct interpretation of the p-value in GreyListChIP?
GreyListChIP
updated 3.3 years ago by ▴ 650 • written 3.3 years ago by ▴ 10
8
votes
20
replies
4.6k
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
updated 2.3 years ago by ★ 5.2k • written 3.4 years ago by ▴ 10
5
votes
10
replies
1.8k
views
Learning DiffBind - some basic questions
DiffBind
updated 3.1 years ago by ★ 5.2k • written 3.4 years ago by ▴ 10
2
votes
1
reply
922
views
Bewildering PCA plot at DiffBind
DiffBind
updated 3.4 years ago by ★ 5.2k • written 3.4 years ago by ▴ 10
0
votes
0
replies
742
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.4 years ago Sam ▴ 10
11
votes
18
replies
4.9k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 3.1 years ago by 50k • written 3.7 years ago by ▴ 10
1
vote
4
replies
1.0k
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 10
0
votes
1
reply
771
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect limma
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 10
1
vote
2
replies
656
views
Why does dispersion estimation in DESeq2 depend on the design formula?
deseq2
updated 4.5 years ago by 42k • written 4.5 years ago by ▴ 10
2
votes
2
replies
1.3k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 4.6 years ago by 42k • written 4.6 years ago by ▴ 10
2
votes
2
replies
1.0k
views
What to do when a bug is found in a BioConductor package (Glimma)
glimma software error
updated 4.7 years ago by 50k • written 4.7 years ago by ▴ 10
0
votes
0
replies
812
views
The correct specification of the model matrix to ComBat
ComBat sva
4.7 years ago Sam ▴ 10
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