Skip to content

Update README.md #26

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update README.md #26

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 5 additions & 7 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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`