molecular-subtyping-neurocytoma

Molecular Subtyping of Neurocytoma

Module authors: Krutika Gaonkar (@kgaonkar6), Jo Lynne Rokita (@jharenza)

In this analysis we subtype Neurocytoma samples according to the primary_site and pathology_diagnosis values. If primary_site == "Ventricles" then subtype is CNC (central neurocytoma) if primary_site != "Ventricles" then subtype is EVN (extraventricular neurocytoma)

Molecular subtyping neurocytoma workflow

Inclusion/exclusion criteria

Samples are included for subtyping if we detect the following strings in the pathology_diagnosis field of histologies-base.tsv:

Neurocytoma

01-neurocytoma-subtyping.Rmd reads in the histology file and adds molecular_subtype for neurocytoma samples as CNC if primary_site == "Ventricles" and EVN if primary_site != "Ventricles"

Run script

bash run_subtyping.sh