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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
756
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
votes
3
replies
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
897
views
Deconvolute bulk RNA-Seq from human epithelial tissue scrapings with immune/blood cell contamination
deconvolution
methods
6.2 years ago
casey.rimland
▴ 150
5 results • Page
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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