DGE_workshop_salmon

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Change to log2FC shrinkage to apeglm following advice in Mike

2

marypiper

Update workflow image with log2FC shrinkage after DE testing

1

marypiper

coef vs contrast?

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https://support.bioconductor.org/p/98833/#98837 See this post about using one or the other. Also see vignette for more info ---

mistrm82

Book is on count modeling with DESeq2 with coding and explanations: https://t.co/wZiCNTEq9u?amp=1.

marypiper

Shorten GO part of functional analysis and some of the code (MP)

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marypiper

See table in slide 4 here - https://hbctraining.github.io/Training-modules/planning_successful_rnaseq/slides/functional_analysis_mp.pdf Consider reducing GO content and making the intro to FA more a about databases.

rkhetani

In "Details regarding PCA are given below (based on materials from StatQuest, and if you would like a more thorough description, we encourage you to explore StatQuest's video and our...

jihe-liu

question from the students, should we add this as a note? https://support.bioconductor.org/p/110307/

mistrm82

make this a 1.5 day workshop?

1

mistrm82

Arguments and functions each on own line and comment all code chunks

3

marypiper