MAGINE_Supplement_notebooks

Supplement notebooks to demonstrate MAGINE. The data set consists of 12 time points across label-free, ph-silac, and silac proteomis, rna-seq, and metabolomics on HL60 cells following exposure to bendamustine.

Notebooks

• supplement_notebook_1_data_exploration.ipynb : ExperimentalData Class demonstration.
• supplement_notebook_2_network_creation_and_exploration.ipynb : Generates data specific network and desmonstrates exploration tools.
• supplement_notebook_3_enrichment_analysis.ipynb : Demonstrates enrichment analysis.
• supplement_notebook_4_agn.ipynb : Generation and exploration of "annotated gene set networks".

Additional files

• Data/bendamustine_data.csv.gz : Experimental data (description in notebook 1).
• run_enrichment.py : code to perform enrichment analysis on entire data set.
• enrichment_output : contains all the output of run_enrichment.py.
• bendamustine_enrichment.csv.gz : Enrichment analysis output.

For any question please visit out gitter channel