diff --git a/README.md b/README.md index c3b5e35..8cf0bd4 100644 --- a/README.md +++ b/README.md @@ -36,10 +36,8 @@ python3 grphin.py -u data/oxidative_stress/txid224308/stress_ppi.csv -d data/oxi ## Analyses -1. Generate 1000 randomized subnetworks with 1000 edge swaps based on stress subnetworks (all species): `python3 generateNetworks.py -s 1000 -i 1000` -2. Count graphlets (all species): `bash countRandomizedNets.sh -a -n 1000` -3. Calculate significance for graphlet occurences based on 1000 randomized networks (all species): `python3 significance.py -i 1000` - -``` - -``` +1. Generate the stress response subnetwork using Random Walk with Restart (all species): +`python3 pageRank.py` +2. Generate 1000 randomized subnetworks with 1000 edge swaps based on stress subnetworks (all species): `python3 generateNetworks.py -s 1000 -i 1000` +3. Count graphlets (all species): `bash countRandomizedNets.sh -a -n 1000` +4. Calculate significance for graphlet occurences based on 1000 randomized networks (all species): `python3 significance.py -i 1000` \ No newline at end of file