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.R Packages: ggplot2, reshape2
Step3_dataWrangling.R Packages: ggplot2, reshape2, dplyr, ggvis
Step4_diffGenes.R Packages: limma, edgeR, SVA, Sleuth
Step5_heatmap.R Packages: gplots, Rcolorbrewer
Step6_geneSetAnalysis.R Packages: GSVA, GSEAbase
markdownSummaryReport.Rmd Packages: Rmarkdown, knitr
server.R, ui.R, global.R, Instructions.md, Abstract.md Packages: shiny, shinyapps, DT