base methods datasets utils grDevices graphics stats knitr tidyverse ggplot2 tibble tidyr readr purrr dplyr stringr forcats lubridate kableExtra DT BiocGenerics stats4 S4Vectors IRanges XVector GenomeInfoDb Biostrings NLP tm pheatmap GenomicRanges matrixStats MatrixGenerics Biobase SummarizedExperiment DESeq2