Code related to the analysis and figure generation for the manuscript:
Hoyd, R., Wheeler, C., Liu, Y., Singh, M. S. J., Muniak, M., Denko, N., Carbone, D. P., Xiaokui, M., & Spakowicz, D. (2022). Exogenous sequences in tumors and immune cells (exotic): A tool for estimating the microbe abundances in tumor RNAseq data (p. 2022.08.16.503205). bioRxiv. https://doi.org/10.1101/2022.08.16.503205
For the {exotic} package installation and usage, see the exotic package repository.
Supplemental figures:
TableS1_survival-results
TableS2_summary_survival-concordance-network
TableS3_network_correlations_top-degcent-mics
TableS4_network_degree-centrality_regression
TableS5_network_closeness-centrality_regression
TableS6_network_betweenness-centrality_regression
TableS7_pathway-enrichment