R scripts

The lectures will be paired with R scripts which will ‘step’ through the process of analyzing transcriptional profiling data from RNAseq experiments

Script Name Comments
readMapping.sh Shell script for ‘walk away’ mapping of reads with Kallisto
Step1_preprocessingKallisto.R Packages: tximport, Biostrings, ensembldb, readr, organism-specific database
Step2_dataExploration_part1.R base R (dist, hclust, prcomp), ggplot2, reshape2
Step3_dataExploration_part2.R dplyr (filter, arrange, select), reshape2 (melt), ggplot2, ggviz
Step4_diffGenes.R Limma (topTable and DecideTests),
Step5_heatmap.R heatmap.2
Step6_geneSetAnalysis.R GSEAbase, GSVA
Step7_Rmarkdown.rmd Rmarkdown, knitr
server.R, ui.R, global.R, Instructions.md, Abstract.md shiny, shinyapps, devtools, DT, ggvis, dplyr