Bioconductor BiovizBase

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biovizBase biovi

updated 2.0 years ago by James W. MacDonald 68k • written 2.0 years ago by bernatgel ▴ 150

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biovizBase ggbio

updated 5.5 years ago by James W. MacDonald 68k • written 5.5 years ago by moldach ▴ 20

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ggbio biovizBase

9.3 years ago kevin.rue ▴ 350

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biovizbase installation

updated 10.8 years ago by Dan Tenenbaum ★ 8.2k • written 10.8 years ago by ville.q.rantanen • 0

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annotate biovizBase ggbio UniProt.ws Pbase annotate biovizBase ggbio UniProt.ws Pbase

updated 11.1 years ago by Tengfei Yin ▴ 490 • written 11.1 years ago by Laurent Gatto 1.6k

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TranscriptDb biovizBase ggbio TranscriptDb biovizBase ggbio

updated 11.9 years ago by Tengfei Yin ▴ 490 • written 11.9 years ago by Malcolm Cook ★ 1.6k

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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?

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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