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GoSemSim - function mgeneSim() is resulting in similarity matrix without 1s on diagonal
GOSim GOSemSim
updated 2.6 years ago by ▴ 760 • written 2.6 years ago by ▴ 10
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I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db GOfuncR GO GOSim goProfiles
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
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compute similarities of GOTerms with GOSim in non-human species
GOSim
updated 6.9 years ago by ▴ 760 • written 6.9 years ago by ▴ 10
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Normalization of specificity level (level of depth) of GO terms dataset
gosim gosemsim
updated 8.5 years ago by ▴ 760 • written 9.9 years ago by ▴ 10
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GOSim yeast
GO Yeast GOSim GO Yeast GOSim
updated 8.5 years ago by • 0 • written 13.3 years ago by ★ 13k
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GOSim Problem
Yeast Organism GOSim Yeast Organism GOSim
12.9 years ago Pablo Andretta Jaskowiak ▴ 10
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Problem while working with GOSim package
GOSim GOSim
13.0 years ago ANIRBAN BHAR ▴ 60
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Simple GO pie and GOSim install error
GO Organism biomaRt GOSim GO Organism biomaRt GOSim
updated 14.0 years ago by ▴ 40 • written 14.0 years ago by ★ 7.2k
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Simple GO pie and GOSim install error
GO Organism biomaRt GOSim GO Organism biomaRt GOSim
14.0 years ago Olivier Lucas ▴ 40
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1.5k
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Query Gene Ontology
GOSim GOSim
updated 14.3 years ago by ★ 13k • written 14.3 years ago by ▴ 10
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1.5k
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Gene ID of yeast in GOSemSim and other GO related package may need update
Annotation GO Yeast biomaRt GOSemSim GOSim Annotation GO Yeast biomaRt GOSemSim GOSim
updated 16.0 years ago by ★ 7.2k • written 16.0 years ago by ▴ 20
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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