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LICENSE.md
MANIFEST.in
README.md
requirements.txt
setup.md
tutorial1_data_intro.ipynb
tutorial2_pandas.ipynb
tutorial3_joining_dataframes.ipynb
tutorial4_multiindex.ipynb
tutorial5_updates.ipynb
usecase1_omics.ipynb
usecase2_clinical_attributes.ipynb
usecase3_clinical_and_acetylation.ipynb
usecase4_mutations_and_omics.ipynb
usecase5_enrichment_analysis.ipynb
usecase6_derived_molecular.ipynb
usecase7_trans_genetic_effect.ipynb

README.md

Tutorials

Tutorials for this package describe how to use the package functions for research with the provided data. All the tutorials are written in Python using the interactive Jupyter notebooks. If you are unfamiliar with Jupyter, follow the instructions given here on the Jupyter website. You will then be able to run our tutorials as interactive, exploratory data analyses.

In general, tutorials are basic coding introduction to the API as well as conventions for storing and accessing the data. The use cases are short examples focused on a biological question and show practical uses of the API for biological discovery.

  • Tutorial 1: CPTAC data introduction
  • Tutorial 2: Using pandas to work with cptac dataframes
  • Tutorial 3: Joining dataframes with cptac
  • Tutorial 4: Understanding multi-indexes
  • Tutorial 5: How to keep up to date with new package and data releases
  • Use Case 1: Comparing transcriptomics and proteomics for a single gene
  • Use Case 2: Looking for correlation between clinical attributes
  • Use Case 3: Associating clinical variables with omics data
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