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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome
methods
GenomicRanges
4.6 years ago
Aditya
▴ 160
0
votes
1
reply
757
views
Why does S4Vectors define three functions for Vector -> data.frame coercion
S4Vectors
methods
4.6 years ago
Aditya
▴ 160
2
votes
2
replies
1.0k
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SetMethod to dispatch on class in unattached package
s4
methods
SummarizedExperiment
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
brendan.innes
▴ 20
0
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3
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1.1k
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How to clear a cached S4 method
devtools
S4
methods
cache
5.4 years ago
Michael Steinbaugh
▴ 90
0
votes
0
replies
898
views
Deconvolute bulk RNA-Seq from human epithelial tissue scrapings with immune/blood cell contamination
deconvolution
methods
6.2 years ago
casey.rimland
▴ 150
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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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