Bioconductor MSIGDB

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659

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GSEABase fgsea msigdb GeneSetEnrichment

11 weeks ago Assa Yeroslaviz ★ 1.5k

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291

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msigdb fgsea msig

5 months ago Tanvi • 0

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545

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geneset GeneSetEnrichment msigdb

7 months ago Seongsu • 0

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644

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msigdb gmt GSEA

written 8 months ago by Georg • 0

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2.1k

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ssgsea GSVA biotype proteincoding msigdb

updated 8 weeks ago by Ginny • 0 • written 12 months ago by snijesh ▴ 200

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1.7k

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msigdb GSEABase GSVA

updated 2.7 years ago by Robert Castelo ★ 3.4k • written 2.7 years ago by forlani.luca • 0

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2.2k

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gseabase msigdb genesetcollection Tutorial

written 6.4 years ago by t.kuilman ▴ 170

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4.7k

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clusterprofiler GSEA MSIGDB

updated 6.7 years ago by Guangchuang Yu ★ 1.2k • written 6.7 years ago by thomasjenner333 • 0

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1.5k

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limma romer msigdb

updated 9.2 years ago by James W. MacDonald 67k • written 9.3 years ago by Jon Manning ▴ 40

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1.5k

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category gostats msigdb hypergeometric test

9.3 years ago petyuk ▴ 70

10 results • Page 1 of 1

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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…

Answer: ANOVA like approach of edgeR by Gordon Smyth 51k

You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…

Votes

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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