An efficient gene regulatory network inference algorithm for early Drosophila melanogaster embryogenesis

Reference

In submission.

Download

git clone https://github.com/hmatsu1226/GRN_linearRD
cd GRN_linearRD

Or download from "Download ZIP" button and unzip it.

Usage

Rscript GRN_linearRD.R <Input_file> <Output_file1> <Output_file2> <s>

• Input_file : G x S matrix of expression data; G is the number of gene, S is the number of position
• Output_file1 : Inferred W.
• Output_file2 : Inferred A (-W*W).
• s : The size of small space step (delta s).

Example of running SCODE

Rscript GRN_linearRD.R data/data_dm.txt W_dm.txt A_dm.txt 0.001

Dataset

The smoothed gap gene expression data. The original expression data is downloaded from SuperFly (http://superfly.crg.eu).

data/data_dm.txt

The smoothed gap gene data (hb, Kr, gt, and kni) of Drosophila melanogaster.

data/data_ca.txt

The smoothed gap gene data (hb, Kr, gt, and knl) of Clogmia albipunctata.

License

Copyright (c) 2017 Hirotaka Matsumoto Released under the MIT license