Shared codes and scripts used in "DNA methylation profile for accurate classification of pediatric sarcomas" Silva, FLT et.al (2024)
Note: Tumor infiltrating leucokytes deconvolution and tSNE analysis depend on Beta-value matrix generated using Minfi R package (R version 4.3.2)
Methylation analysis to obtain Beta value Matrix, TILs deconvolution, tSNE and Copy Number Alterations were run using R paackages. Fusion genes calling was run in Linux environment (GNU/Linux 6.5.0-21-generic x86_64)
Please read packages instructions before running:
Sarcoma Classifier (v12.2) and Brain Classifier (mnp v12.5):https://www.molecularneuropathology.org/mnp/
Minfi: https://bioconductor.org/packages/release/bioc/html/minfi.html
Conumee2.0: https://github.com/hovestadtlab/conumee2
STAR-FUSION: https://github.com/STAR-Fusion/STAR-Fusion
ChimeraViz: https://www.bioconductor.org/packages/devel/bioc/vignettes/chimeraviz/inst/doc/chimeraviz-vignette.html
pheatmap: https://cran.r-project.org/web/packages/pheatmap/index.html
MethylResolver: https://github.com/darneson/MethylResolver