knitr tidyverse ggplot2 tibble tidyr readr purrr dplyr stringr forcats lubridate kableExtra BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges matrixStats MatrixGenerics Biobase SummarizedExperiment DESeq2 pheatmap RColorBrewer data.table DT BiocParallel XVector Biostrings Rsamtools GenomicAlignments ShortRead