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biomaRt connection sql

updated 3.6 years ago by Joan Miró ▴ 80 • written 3.6 years ago by Anand ▴ 10

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MakeOrgPackageFromNCBI NCBI SQL AnnotationForge

updated 4.6 years ago by James W. MacDonald 67k • written 4.6 years ago by chefer • 0

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R shell Python SQL Job

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biomedical informatics data science python SQL Job

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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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