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sfanalysis's Introduction

Scale-free network analysis

This repo contains the code for analyzing scale-free patterns in networks as described in this paper. The data sets used in the paper are in the degreesequences directory.

Citation information

If you use this code in your research, please cite this repo and/or the paper (linked above):

Anna D. Broido & Aaron Clauset, "Scale-free networks are rare", Nature Communications 10, 1017 (2019).

Usage

There are two ways to use this repo:

  1. extract degree sequences from network data in the form of gml files and then analyze these for scale-free patterns

  2. given degree sequences in the appropriate format (examples in the degree sequences folder), sort them into scale-free categories. Without gml information, this version of the pipeline treats each degree sequences as belonging to a unique network.

Dependencies

The code is written in Python2 and will not work in Python3. Additionally, the following packages must also be installed:

  • NumPy
  • Pandas
  • SciPy
  • mpmath
  • python-igraph

A simple usage example

With GML files

import sys
import pandas as pd
sys.path.append('../code/')
import sfanalysis as sf

# location of gml files to analyze
gml_dir = 'gmls/'
# location to write degree sequences
deg_dir = 'degseqs/'
# make catalog of gmls and write degree sequence files
# each row of deg_df is a degree sequence file
deg_df = sf.write_degree_sequences(gml_dir, deg_dir)
# analyze all degree sequences (this will take a while for many or large data sets)
analysis_df = sf.analyze_degree_sequences(deg_dir, deg_df)
# categorize networks (by unique gml file) into scale-free categories
hyps_df = sf.categorize_networks(analysis_df)

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sfanalysis's Issues

Understanding results of the example

Hello!
First, thanks for giving this repository to test the analysis.

I've succeeded to run an example in the notebook, and got the following result.

I am wondering the result I got is correct.

New question

Good afternoon!

Can you provide me the network edge lists / adjacency matrixes from which the degree sequences were extracted?

Thank you in advance,
Mate

only degree sequences

Hi,

I have two degree sequences whose I want to test their scale-free properties. These files have one column with the names of genes and the count column with the degree.
One file includes all the genes of my PPI network and the other includes a subset of these genes. Basically I want to check if there is any differences in term of scale-free between the whole network and a subset of genes of my interest.

In the usage section, there is written that it is possible to run the code without the gml file.

Could I ask you to provide an example about using the code without the gml information?

I tried to use the 'analyze_degree_sequences' function with only the deg_dir, but the function needs two arguments.

Thank you!

question

Hello, I read your paper and I am trying to evaluate my data set based on your tool. Could you please help me with a pipeline of the functions that need to be executed or an example? Thank you

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