My goal with these templates is to provide a basic pipeline template for reproducible analysis.
Files:
vanillaAnalysisTemplate.Rmd - basic .Rmd outline to help keep me accountable
runDEseq.R - creates the Rdata input for analysis.Rmd
RNAseqAnalysis.Rmd - creates several type of plot including:
-PCA plot
-MA plot
-Volcano plot
-Heatmaps
Libraries Used:
ggplot2
DESeq2
matrixStats
gplots
RColorBrewer
parallel
lattice
plyr
gtools
dplyr
tidyr
kiRsten (available here )
knitr