Bioconductor Gmap

Showing : gmap • reset

1

vote

1

reply

1.2k

views

limma gmap shRNA dropout screen

updated 9.3 years ago by Aaron Lun ★ 29k • written 9.3 years ago by Anna Dvorkin ▴ 40

1 result • Page 1 of 1

Recent ...

Replies

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…

Votes

Answer: Limpa Pipeline Order

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

Awards • All