Bioconductor Topaseq

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ToPASeq Deprecation

2.6 years ago pgauthi1 • 0

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843

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topaseq

updated 6.4 years ago by Gordon Smyth 51k • written 6.5 years ago by Aditya Saxena ▴ 10

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1.1k

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ToPASeq SPIA pathway analysis R

6.7 years ago fawazfebin ▴ 60

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1.1k

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topaseq

updated 7.1 years ago by Martin Morgan 25k • written 7.1 years ago by Aditya Saxena ▴ 10

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1.8k

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installation package installation topaseq igraph LD_LIBRARY_PATH

7.8 years ago jan.soderman • 0

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992

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ToPASeq

updated 7.9 years ago by theobroma22 ▴ 10 • written 7.9 years ago by rubi ▴ 110

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1.5k

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rnaseq Topaseq

8.6 years ago saamar.rajput • 0

7 results • Page 1 of 1

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Comment: Create Illmina bead summary data by Liu • 0

Hi! Yes, thank you! I completely agree. I am just curious about how these two files are processed with AVG_Gre and detection p-value. I am …

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…

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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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