teslajoy/hnscc-macOS

co-expression *analysis pipeline of HNSCC progression features

Coexpression and CoSpliceEx weighted network analysis of Head and Neck Squamous Cell Carcinoma (HNSCC).

We analyzed 229 patients’ samples from The Cancer Genome Atlas (TCGA) previously annotated by Bornstein et al (2016) on their progression status.

Publication

Frontiers Genomics - Systems Biology: ORIGINAL RESEARCH ARTICLE

doi: 10.3389/fgene.2018.00183

https://www.frontiersin.org/articles/10.3389/fgene.2018.00183

OHSU SCHOLAR ARCHIVE: Full Thesis Research

doi:10.6083/M4WQ02WM

https://digitalcommons.ohsu.edu/etd/3824/

Step-by-step study workflow for identification of progressor gene signatures

Dependencies

R version 3.3.1 or 3.3.2

Credits

• Ovidiu Dan Iancu open access research and code
• WGCNA
• Bornstein et al. study (2016)
• TCGA
• Hadley Wickham Data Science, Data import, and R software engineering libraries

Note

This code was written over a short period of time to complete educational milestones and should not be taken as a computationally automated process/pipeline. However, each code segment (between code comments) may be repurposed. The publication requires this code to be public.