CellNOpt.CORE documentation

cellnopt.core

Motivation

Cellnopt.core is a pure Python library that provides core functions to manipulate signalling data. It provides functions to create and manipulate networks that can be used later on with MIDAS files (phosphorylation measurements). You can read/write data formats such as SIF and MIDAS that are used in CellNOptR.

It does not provide any logical formalism to simulate or optimise the network to the data. It is rather intended to be a package dedicated to the pre and post processing of signalling pathways.

Installation

cellnopt.core has a dependencies on pandas, which requires cython. So, you need to install cython first.

All other dependencies should be installed automatically (networkx, numpy, matplotlib).

pip install easydev
pip install cython
pip install cellnopt.core

User guide

• 1. Quick Start
  • 1.1. The CNOGraph data structure
  • 1.2. Read data files in SIF and MIDAS formats
• 2. User Guide
  • 2.1. The different formats
  • 2.2. The CNOGraph data structure and plotting
• 3. MISC code
  • 3.1. Renames nodes in a graph and combining several graph

References

• 1. Data Structures
  • 1.1. CNOgraph module
  • 1.2. MIDAS related
  • 1.3. SIF
• 2. Converters
  • 2.1. SIF2ASP module
  • 2.2. asp module
  • 2.3. ADJ2SIF module
  • 2.4. SOP2SIF module
  • 2.5. EDA module
• 3. Others
  • 3.1. Interaction class
  • 3.2. kinexus
  • 3.3. Reactions module
  • 3.4. Metabolites module

• Biblio

• ChangeLog
• FAQS
• How do the logical symbols are coded ?