Bioconductor Seqarray

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seqArray seqVCF2GDS

updated 4.6 years ago by Stephanie M. Gogarten ▴ 890 • written 4.6 years ago by ealopera • 0

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software error SeqArray seqVCF2GDS

updated 5.4 years ago by zhengx ▴ 30 • written 5.4 years ago by winstondunnmd ▴ 10

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SeqArray

updated 5.8 years ago by zhengx ▴ 30 • written 5.8 years ago by miyouduniu • 0

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genesis gwastools seqarray

6.2 years ago • updated 5.9 years ago Stephanie M. Gogarten ▴ 890

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seqarray

updated 6.4 years ago by Stephanie M. Gogarten ▴ 890 • written 6.4 years ago by cav3gh • 0

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SeqArray info SeqArray::info()

7.0 years ago qliu7 • 0

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

They provide the code they used for DGE analysis in a gitlab link that can be found in the paper. In there you can find: ```` # estimate d…

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

It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…

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

Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…

Comment: PCA of different bacterial species by Jeremy • 0

Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…

Comment: RnBeads::combine() - error? by Urotree • 0

pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…

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

Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis

scater/scran with TPMs from Salmon - counts?

A: Full length single-cell RNA-seq - tximport output for downstream analysis

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