Bioconductor Loop

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loop deseq2 rnaseq

updated 2.4 years ago by chm • 0 • written 4.8 years ago by NeuroGeneticsBoy ▴ 10

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loop filter

written 7.0 years ago by kritikamish99 ▴ 10

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loop matix

updated 8.8 years ago by Martin Morgan 25k • written 8.8 years ago by Arman Shahrisa ▴ 20

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apply for loop

9.0 years ago KB ▴ 50

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command line automation loop

9.3 years ago ChIP-Tease • 0

5 results • Page 1 of 1

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Answer: Epic v2 Annotation CpG_maf source? by James W. MacDonald 67k

Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…

Comment: Deseq2 res Function by James W. MacDonald 67k

In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…

Answer: Struggle with the replicates of epic array data by James W. MacDonald 67k

You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …

Comment: Identifying potentially associated gene set to drug response using GSVA by Robert Castelo ★ 3.4k

So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…

Answer: Deseq2 res Function by Michael Love 43k

> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…

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Appropriate use of the function treat of the limma package

Comment: Is it recommended to analyze different tissues together when using edgeR

Answer: Deseq2 res Function

Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification

Answer: ANOVA like approach of edgeR

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