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Compute GSVA using matrisome gene list, then plot samples #10

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sgosline opened this issue Jan 22, 2021 · 0 comments

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sgosline commented Jan 22, 2021

Related to #9, we want to evaluate the overall expression of all genes in the matrisome lists. To do this, we need to run the GSVA package.

1- download/install the GSVA tool:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-7 https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
2- convert the Matrisome gene sets to gene lists (the tool should tell you how)
3- assign each sample its own matrisome score based on the output of GSVA - this should be an x by y matrix where x is the number of matrisome lists and y is the number of samples
4- cluster the scores in a heatmap!

sgosline assigned jessbade

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