Workflow code supporting the manuscript 'Assessing Individual Head and Neck Squamous Cell Carcinoma Patient Response to Therapy Through Integration of Functional and Genomic Data'
Files required for the data folder:
Files can be downloaded from https://github.com/biodev/hnscc_data
- hnscc_clinical.txt
- hnscc_inhibitor_data.txt
- hnscc_targetome_subset.txt
- hnscc_wes_somatic_calls.txt
- hnscc_gene_cna_calls.txt
- hnscc_rnaseq_counts.txt
- hnscc_rna_annots.txt
- hnscc_rppa.txt
- hnscc_rppa_abs.txt
- wgcna_mm.txt
- tcga_plus_hnscc_exprs.txt.gz
- hnscc_netprop_results.txt
Distributed as part of this repo:
- Derived from the TCGA-HNSC manuscript and licensed under the terms of the corresponding manuscript.
- data/tcga_targetable_genes.xlsx -- Genes and pathways from Figure 3
- data/putative_drivers_tcga_gistic_regions.xlsx -- Formed from the highlighted genes in Supplemental Data S2.1
- data/tcga_mut_freq.xlsx -- Significant (q < 0.1) genes and frequencies from Figure 2
Also need to supply the following files in the external folder:
- Reactome FIs
- FIsInGene_070323_with_annotations.txt
- Genomic Data Commons (TCGA-HNSC):
- classification_centroid_728genes.txt
- all_thresholded.by_genes
- TCGA-HNSC Supplementary Data
- nature14129-s2/7.2.xlsx
- nature14129-s2/4.1.xlsx
- Iorio et al 2016 Supplmental Information
- TableS4C.xlsx
- Genomics of Drug Sensitivity in Cancer
- GDSC1_fitted_dose_response_27Oct23.xlsx
- GDSC2_fitted_dose_response_27Oct23.xlsx
- screened_compounds_rel_8.5.csv
- Cell Model Passports
- mutations_summary_20230202.csv
- cnv_gistic_20191101.csv
- model_list_20240110.csv
- Hallmarks
- h.all.v7.5.1.symbols.gmt
- Entrez gene info file
- Homo_sapiens.gene_info.gz
- PanCancer Pathways
- mmc3.xlsx
This workflow uses the targets R package. To run simply use the command:
targets::tar_make()
R version 4.4.2
| Package | Version |
|---|---|
| targets | 1.9.0 |
| clusterProfiler | 4.14.3 |
| ComplexHeatmap | 2.22.0 |
| ConsensusClusterPlus | 1.70.0 |
| edgeR | 4.4.0 |
| ggplot2 | 3.5.1 |
| ggrepel | 0.9.6 |
| igraph | 2.1.1 |
| openxlsx | 4.2.7.1 |
| patchwork | 1.3.0 |
| RColorBrewer | 1.1-3 |
| tidyverse | 2.0.0 |
| uwot | 0.2.2 |
| extrafont | 0.19 |
This code was developed by Daniel Bottomly, a member of the McWeeney Lab and is protected under copyright by the Oregon Health and Science University Knight Cancer Institute, 2024.