Bioconductor GenVisR

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GenVisR GenCov

2.3 years ago Amy_ • 0

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GenVisR GenVis

updated 14 months ago by zlskidmore ▴ 30 • written 2.5 years ago by abhisikta • 0

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Install mainDropMut GenVisR

updated 2.6 years ago by Hervé Pagès 16k • written 2.6 years ago by Michel • 0

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GenVisR maftools

2.6 years ago e • 0

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variants waterfall GenVisR

updated 4.2 years ago by zlskidmore ▴ 30 • written 4.2 years ago by Jeni ▴ 10

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GenVisR ggplot2 waterfall

5.2 years ago sheneicechang • 0

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GenVisR mutation frequency R cancer bioconductor

5.3 years ago sheneicechang • 0

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GenVisr genvisr waterfall mutation

updated 6.1 years ago by zlskidmore ▴ 30 • written 6.2 years ago by ZihaoXing • 0

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genvisr lohSpec

6.5 years ago dharia.priyadarshani • 0

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genvisr

6.6 years ago cedric.vmdl • 0

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GenVisR

7.0 years ago daijieqiong ▴ 10

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GenVisR

updated 7.9 years ago by zlskidmore ▴ 30 • written 7.9 years ago by Bogdan ▴ 670

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genvisR

8.9 years ago • updated 8.8 years ago Deep Adhya ▴ 20

13 results • Page 1 of 1

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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

I edited the previous post. I meant to remove the estimateGLMRobustDisp line in the second snipper : ```` DGE_list_object <- estimateGLMR…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Sorry, I had forgotten estimateGLMDisp() produces weights as well as NB dispersions. The weights from estimatGLMRobustDisp() were intended …

Answer: Mean variance curve troubleshoot filtering by Gordon Smyth 52k

You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…

Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k

You will get NA coefficients from `~Group+Batch` because the Group factor is completely confounded with the batch factor.

Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0

Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…

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Comment: Comparing different method for DESEQ2

Answer: How do I fix an odd voom plot in a combined dataset?

Comment: How do I fix an odd voom plot in a combined dataset?

C: How does edgeR cpm function calculate log(CPM) values?

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