base methods datasets utils grDevices graphics stats knitr tidyverse ggplot2 tibble tidyr readr purrr dplyr stringr forcats lubridate dynamicTreeCut fastcluster WGCNA magrittr genefilter stats4 BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges matrixStats MatrixGenerics Biobase SummarizedExperiment DESeq2 ggfortify RColorBrewer pheatmap factoextra permute lattice vegan dendsort grid ComplexHeatmap psych igraph ggraph