burtonjosh / osconet.jl

Detect oscillatory gene networks from snapshot single-cell data

OscoNet.jl: inferring oscillatory gene networks

A Julia implementation of OscoNet¹, a method for detecting oscillatory gene networks from snapshot single cell data. For more details, see the paper.

Installation

Open the Julia REPL by typing the following in the command line:

$ julia

Enter the Pkg REPL by typing ] from the Julia REPL.

julia> ]

To install OscoNet, type the following into the Pkg REPL

(@v1.6) pkg> add "https://github.com/burtonjosh/OscoNet.jl.git"

To exit the Pkg REPL either press backspace or ^C (CTRL+C).

You can now start using the OscoNet package,

julia> using OscoNet

Usage

Basic usage of the package:

using OscoNet
data, _, _ = simulate_data();
n_permutations = 100;

adjacency_matrix, _, cost = bootstrap_hypothesis_test(data, n_permutations);

gene_names = ["gene_$i" for i = 1:20];

edge_network = create_edge_network(adjacency_matrix, 1 ./ cost, gene_names)

For more details and examples, refer to the package documentation.

Footnotes

1. Luisa Cutillo, Alexis Boukouvalas, Elli Marinopoulou, Nancy Papalopulu & Magnus Rattray (2020). OscoNet: inferring oscillatory gene networks. BMC Bioinformatics: 10.1186/s12859-020-03561-y. Code ↩