Welcome to CanDI’s documentation!

Contents:

• CanDI - A global cancer data integrator
  • Installation
  • Usage
  • Citation

Package:

• Module Structure:
  • CanDI.candi module
  • CanDI.data module

Notebooks:

• Getting Started
  • Importing
  • Data Object
  • How to Directly Load a Dataset
  • Cell Lines
  • Genes
  • Locations
  • Basic Object Instantiation
  • Gene Object Methods and Attributes
  • Gene Indexing examples
  • CellLine Methods and Attributes
  • Cancer Methods and Attributes
  • Organelle Methods and Attributes
• BRCA Heatmap
  • Cancer Object Instantiation
  • Subsetting by mutation status
  • Cross Referencing Mutation and Gene Knockout Data
  • Fanconi Anemia Genes Knockout Effect in Ovarian Cancer
  • Fanconi Anemia Genes Knockout Effect in Breast Cancer
• KRAS and EGFR Scatter plot
  • Cancer Object Instantiation
  • Analyzing Global Gene Dependency
  • Note about Gene Effect Scores: Dependency vs Essentiality
• CanDI and DESeq2
  • Object Instantiation
  • Data Munging
  • Running pyDESeq2
  • Analyzing Results

Indices and tables

• Index

• Module Index

• Search Page