This repository contains code for reproducing the results and figures presented in the paper "Identifying Sex Differences in Lung Adenocarcinoma Using Multi-Omics Integrative Protein Signaling Networks."
R version 4.3.0 or later is required. Below are the R package version requirements:
Click to view full package dependencies
| Package | Version |
|---|---|
| dplyr | 1.1.2 |
| GenomicDataCommons | 1.24.3 |
| plyr | 1.8.8 |
| tidyverse | 2.0.0 |
| impute | 1.74.1 |
| reticulate | 1.31 |
| bigstatsr | 1.5.12 |
| data.table | 1.14.8 |
| dorothea | 1.12.0 |
| ggplot2 | 3.4.2 |
| recount | 1.26.0 |
| sva | 3.48.0 |
| edgeR | 3.42.2 |
| recount3 | 1.10.2 |
| biomaRt | 2.56.0 |
| cmapR | 1.14.0 |
| ssGSEA2 | 1.0.0 |
| netZooR | 1.3.15 |
| OmnipathR | 3.8.0 |
| TIGER | 0.0.0.9000 |
| limma | 3.56.1 |
| SummarizedExperiment | 1.30.1 |
| BioEnricher | 0.1.0 |
| clusterProfiler | 4.8.3 |
| org.Hs.eg.db | 3.17.0 |
| ggpubr | 0.6.0 |
| scales | 1.2.1 |
| pheatmap | 1.0.12 |
| viridis | 0.6.4 |
| ggupset | 0.3.0 |
| HGNChelper | 0.8.1 |
| ggforce | 0.4.1 |
| ggraph | 2.1.0 |
| graphlayouts | 1.0.0 |
| igraph | 1.4.3 |
| scatterpie | 0.2.1 |
| tibble | 3.2.1 |
| tidygraph | 1.2.3 |
| glmnet | 4.1.8 |
| stringr | 1.5.0 |
| cowplot | 1.1.1 |
| purrr | 1.0.1 |
| survival | 3.5.5 |
| survminer | 0.4.9 |
| table1 | 1.4.3 |
| matrixStats | 0.63.0 |
| matrixTests | 0.2.2 |
If you have any questions or feedback, please feel free to reach out to us at [email protected]