Reproducibility statement

This book is compiled with R 4.0.0 and the following packages. We only list the main packages and their versions but not their dependencies.

## qvalue_2.20.0 | plot3D_1.3 | ggplot2_3.3.1 | pheatmap_1.0.12
## cowplot_1.0.0 | cluster_2.1.0 | NbClust_3.0 | fastICA_1.2.2
## NMF_0.23.0 | matrixStats_0.56.0 | Rtsne_0.15 | mosaic_1.7.0
## knitr_1.28 | genomation_1.20.0 | ggbio_1.36.0 | Gviz_1.32.0
## DESeq2_1.28.1 | RUVSeq_1.22.0 | gProfileR_0.7.0 | ggfortify_0.4.10
## corrplot_0.84 | gage_2.37.0 | EDASeq_2.22.0 | citr_0.3.2
## formatR_1.7 | svglite_1.2.3 | Rqc_1.22.0 | ShortRead_1.46.0
## QuasR_1.28.0 | methylKit_1.14.2 | FactoMineR_2.3 | iClusterPlus_1.24.0
## enrichR_2.1 | caret_6.0.86 | xgboost_1.0.0.2 | glmnet_4.0
## DALEX_1.2.1 | kernlab_0.9.29 | pROC_1.16.2 | nnet_7.3.14
## RANN_2.6.1 | ranger_0.12.1 | GenomeInfoDb_1.24.0 | GenomicRanges_1.40.0
## GenomicAlignments_1.24.0 | ComplexHeatmap_2.4.2 | circlize_0.4.9 | rtracklayer_1.48.0
## tidyr_1.1.0 | AnnotationHub_2.20.0 | GenomicFeatures_1.40.0 | normr_1.14.0
## MotifDb_1.30.0 | TFBSTools_1.26.0 | rGADEM_2.36.0 | JASPAR2018_1.1.1
## BSgenome.Hsapiens.UCSC.hg38_1.4.3 | BSgenome.Hsapiens.UCSC.hg19_1.4.3