Skip to content

Commit

Permalink
Updated README: included link to pypath github repo.
Browse files Browse the repository at this point in the history
  • Loading branch information
jakob-wirbel committed Jul 5, 2016
1 parent 134b023 commit 50644a3
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions README.md
Expand Up @@ -33,17 +33,17 @@ A0FGR8_S691 0.271458 0.264596 0.501685 0.461984 0.655501
A0JLT2_S2260.080786 1.069710 0.519780 0.5208830.296040
```

Prior-knowledge information about kinase-substrate interactions can be loaded from the `pypath` package (see also the [documentation](http://omnipathdb.org/)).
Prior-knowledge information about kinase-substrate interactions can be loaded with the `pypath` package (see also the [documentation](http://omnipathdb.org/) or the [github repository](https://github.com/saezlab/pypath)).
```python
adjacency_matrix = kinact.get_kinase_targets(sources=['all'])
```

Finally, estimation of the kinase activities can be performed as follows for the example of the KSEA protocol:
```python
scores, p_values = kinact.ksea.ksea_mean(data_fc=data_fc["5min"].dropna(),
interactions=adjacency_matrix,
mP=data_fc["5min"].values.mean(),
delta=data_fc["5min"].values.std())
interactions=adjacency_matrix,
mP=data_fc["5min"].values.mean(),
delta=data_fc["5min"].values.std())
```

## Methods included in kinact:
Expand Down

0 comments on commit 50644a3

Please sign in to comment.