hnscc-macos
co-expression *analysis pipeline of HNSCC progression features
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 7 DOI reference(s) in README -
✓Academic publication links
Links to: frontiersin.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (7.5%) to scientific vocabulary
Repository
co-expression *analysis pipeline of HNSCC progression features
Basic Info
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
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.
Owner
- Name: Nasim Sanati (Rieker)
- Login: teslajoy
- Kind: user
- Location: United States
- Website: https://teslajoy.github.io/bio/
- Twitter: teslajoys
- Repositories: 2
- Profile: https://github.com/teslajoy
Citation (CITATION.cff)
cff-version: 1.0.0 message: "In case of using the methods, data, and/or software, please cite as below." authors: - family-names: "Sanati" given-names: "Nasim" - family-names: "Iancu" given-names: "Ovidiu" - family-names: "Guanming" given-names: "Wu" - family-names: "Jacobs" given-names: "James" - family-names: "McWeeney" given-names: "Shannon" title: "Network-based predictors of progression in head and neck squamous cell carcinoma" version: 1.0.0 doi: 10.3389/fgene.2018.00183 date-released: 2018-05-29 url: "https://github.com/teslajoy/hnscc-macOS"