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Here will be a general guide to bulk transcriptomic analysis. This is a collection of resources we've found useful when analyzing bulk transcriptomic data. We also have analysis pipelines (coming soon) on the website.
General Guides
General Guides
Guides and Vignettes
Bulk RNAseq Pipeline: an computaional walkthrough going from data on GEO to differential expression with DESeq2 and gene set enrichment analysis.
Bulk RNAseq Background: an online walkthrough of bulk transcriptomic sequencing and analysis. Provides good background but doesn't include code.
DESeq2 Vignette: DESeq2 is a popular tool used for normalization, differential expression and plotting of bulk RNAseq. Requires count data.
Limma Vignette: Limma is another popular tool used for normalization and differential expression. Unlike DESeq2 it doesn't require count data. Chapter 15 shows the usage in RNA-Seq data.
Videos:
A Practical Guide to Bulk RNAseq: a general overview of bulk RNAseq analysis and what tools are available.
Beginner's Guide to Bulk RNA-Seq Analysis: a general guide/overview
DESeq2 Walkthrough: walkthrough of DESeq2 with coding
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