About MIDAS

MIDAS is a software tool that determines differentially activated subpaths from multi-class RNA-seq data.

Highrights

• MIDAS utilizes explicit gene expression quantity information from RNA-seq.
• MIDAS extends a recent edge activation measurement technique for determining subpaths with differential activities.
• MIDAS uses the multi-class issue in a statistical approach.
• MIDAS uses a greedy subpath extension method with exponentially increasing criteria.

Installation

MIDAS is implemented in with Bash scripts, R, and Python libraries. Belows are requirements for MIDAS.

Requirements

• Python: 2.7
• Networkx: over 1.10 (https://networkx.github.io/index.html)
• scipy: over 0.17.1 (https://www.scipy.org/)
• Statsmodels: over 0.6.1 (http://www.statsmodels.org/0.6.1/index.html)
• matplotlib: over 1.5.1 (http://matplotlib.org/)
• R: over 3.0.2

Usage

First, clone the repository or download compressed source code files.

$ git clone https://github.com/bhi-kimlab/MIDAS.git
$ cd MIDAS

You can see the valid paramenters for MIDAS by help option:

$ bash ./run.sh --help

One example of parameter setting is like:

$ bash run.sh \
		 --expression ./test_data/total_exp.MGD \
		 --pathway_set ./test_data/pathway_set.txt \
		 --class_info ./test_data/total_exp.MGD.sample_class.txt \
		 --output_directory ./test_result/ \
		 --start_threshold 0.05 \
		 --increase_moment 1e-15 \
		 --permutation_cutoff 0.1 \
		 --permutation_number 100000 \
		 --parallel_cores 10

You can run MIDAS with test data:

cd test
bash ./test_run.sh

Contact

If you have any question or problem, please send a email to sangseon486@snu.ac.kr