Bioconductor Shrna

Showing : shrna • reset

votes

replies

1.9k

views

edger shrna

8.5 years ago sirintra ▴ 10

votes

replies

2.3k

views

shrna edger deseq2 differential expression normalized counts

9.1 years ago Jane Merlevede ▴ 90

vote

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

votes

replies

2.0k

views

edgeR processamplicons shrna

updated 9.8 years ago by thomas.leete • 0 • written 9.9 years ago by Anne Deslattes Mays ▴ 10

votes

replies

3.1k

views

shRNAseq edgeR shRNA

updated 10.0 years ago by Gordon Smyth 53k • written 10.0 years ago by KB ▴ 50

5 results • Page 1 of 1

Recent ...

Replies

Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

Comment: voomLmFit fitted log-CPM values by Lina ▴ 10

Is the output from fitted(v) in the log2 CPM scale? or CPM scale?

Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k

Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```

Votes

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?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

Awards • All