Bioconductor ToPASeq

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ToPASeq Deprecation

3.4 years ago pgauthi1 • 0

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990

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topaseq

updated 7.2 years ago by Gordon Smyth 53k • written 7.2 years ago by Aditya Saxena ▴ 10

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1.2k

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ToPASeq SPIA pathway analysis R

7.4 years ago fawazfebin ▴ 60

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topaseq

updated 7.9 years ago by Martin Morgan 25k • written 7.9 years ago by Aditya Saxena ▴ 10

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installation package installation topaseq igraph LD_LIBRARY_PATH

8.6 years ago jan.soderman • 0

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1.1k

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ToPASeq

updated 8.7 years ago by theobroma22 ▴ 10 • written 8.7 years ago by rubi ▴ 110

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rnaseq Topaseq

9.4 years ago saamar.rajput • 0

7 results • Page 1 of 1

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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

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