Bioconductor Exome

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edgeR exome

updated 5.7 years ago by Aaron Lun ★ 28k • written 5.7 years ago by am3 • 0

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whole exome sequence R bioconductor exome

7.9 years ago • updated 7.8 years ago bioinf ▴ 10

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rsamtools whole exome sequence bam exome R

7.9 years ago bioinf ▴ 10

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exome dnaseq WES

8.6 years ago arvand.akbari • 0

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cnv exome

8.8 years ago Bio152 ▴ 150

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Comment: minfi latest update for EPIC V2 chip by macdonaldfrench7286566 • 0

Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo. *Th…

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

To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

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