This repository contains R scripts for the analysis described in the article "Decoupling epithelial-mesenchymal transitions from stromal profiles by integrative expression analysis". All analysis for this study was performed using R version 3.6.3 (“Holding the Windsock”). The following table shows the packages used, with version numbers.
| R package | Version |
|---|---|
| AnnotationDbi | 1.48.0 |
| caTools | 1.18.0 |
| cluster | 2.1.0 |
| colorspace | 1.4.1 |
| cowplot | 1.0.0 |
| data.table | 1.12.8 |
| dbscan | 1.1.5 |
| egg | 0.4.5 |
| fpc | 2.2.5 |
| ggdendro | 0.1.20 |
| ggplot2 | 3.3.0 |
| ggrepel | 0.8.2 |
| grDevices | 3.6.3 |
| grid | 3.6.3 |
| gridExtra | 2.3 |
| gtable | 0.3.0 |
| infercna | 1.0.0 |
| latex2exp | 0.4.0 |
| limma | 3.42.2 |
| magrittr | 1.5 |
| Matrix | 1.2.18 |
| org.Hs.eg.db | 3.10.0 |
| plyr | 1.8.6 |
| purrr | 0.3.4 |
| RColorBrewer | 1.1.2 |
| Rtsne | 0.15 |
| readxl | 1.3.1 |
| scales | 1.1.1 |
| scater | 1.14.6 |
| scran | 1.14.6 |
| seriation | 1.2.8 |
| SingleCellExperiment | 1.8.0 |
| stringdist | 0.9.6.3 |
| stringi | 1.5.3 |
| stringr | 1.4.0 |