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