Repository of functions used to analyze publicly-available neuroblastoma gene expression datasets.
So far, I have uploaded functions to analyze the TARGET neuroblastoma gene expression dataset. For more information on the TARGET neuroblastoma initiative, please see: https://ocg.cancer.gov/programs/target/projects/neuroblastoma. The data can be downloaded directly from the cBio Portal at: https://www.cbioportal.org/study/summary?id=nbl_target_2018_pub.
I suggest downloading all files in this repository and saving them to a single directory. All functions for analyzing TARGET data are included in the 'TARGET_Analysis_Functions_v2.ipynb' file. In order to run the functions in this file, you need the 'neuroblastoma_gene_expression_analysis_files' folder saved in the same directory. For a tutorial on how to use the functions, please see the 'TARGET_Analysis_Tutorial.ipynb' file.
All .ipynb files are meant to be run on Jupyter Notebook using Python 3.
If you have any questions, please email me at brandon.bergsneider20@imperial.ac.uk