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LieberInstitute / SPEAQeasy-example

Full length example for SPEAQeasy
http://research.libd.org/SPEAQeasy-example
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Code for differential expression analysis and EDA #6

Closed lcolladotor closed 3 years ago

lcolladotor commented 4 years ago

Create a directory and Rmd that uses the output of #5 as the input. Then show how to explore the data (PCA), check the ERCCs (Nick can do this part), normalize the data, perform a differential expression analysis using limma-voom, find enriched ontologies using clusterProfiler and make some heatmaps likely using pheatmap. This could be our own LIBD jaffelab guide for differential expression analyses. Feel free to link to Bioconductor workflows and package vignettes as well. You could also use jaffelab::agePlotter() for example. Use the same BiocStyle and knitcitations style as in #5 for the Rmd (with also the output from sessioninfo::session_info()).

joshstolz commented 4 years ago

I updated a differential expression script to run on the sample files. We may want to look at the model and pca but for now this holds as an example script.

lcolladotor commented 3 years ago

Hi @joshstolz, can you verify whether it's ok to close this issue? Thanks!

joshstolz commented 3 years ago

Yeah we finished that up.

From: Leonardo Collado-Torres @.***> Sent: Saturday, May 1, 2021 10:22:55 PM To: LieberInstitute/SPEAQeasy-example Cc: Josh Stolz; Mention Subject: Re: [LieberInstitute/SPEAQeasy-example] Code for differential expression analysis and EDA (#6)

Hi @joshstolzhttps://github.com/joshstolz, can you verify whether it's ok to close this issue? Thanks!

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