2024-07-31

Accompaniment to "Molecular Characterization of Gliomas and Glioneuronal Tumors Amid Noonan Syndrome: Cancer Predisposition Examined", published in Frontiers in Oncology, August 2024.

This script produces a static and an interactive, annotated UMAP plot of internal and external (UCSC Treehouse CNS) RNASeq cohorts.

User adds internal sample metadata to the metadata/metadata_internal_cohort.xlsx file. The script RNAseq_dimensionality_reduction.R takes as variables the case name, the sample name, and the path to the salmon files. 

To use Treehouse data as external cohort for analysis, we regret to inform you that you must download the dataset. It was too large to upload to Github. 

R/Package versions:
R (4.1.1)
tidyverse (v.1.3.1)
dplyr (v.1.0.9)
plyr (v.1.8.7)
Salmon (v.1.9.0)
tximport (v.1.18.0)
matrixStats (v.0.61.0)
umap (v.0.2.8.0)
rsvg (v.2.2.0)
ggrepel (v.0.9.1)
RColorBrewer (v.1.1.3)
plotly (v.4.10.0)
ggplot2 (v.3.3.6)



For questions regarding this script, please contact [email protected]