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deeenes committed Oct 16, 2024
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Expand Up @@ -19,8 +19,8 @@ An `R` client for the **OmniPath** web service and many other resources.

<https://omnipathdb.org/>

The web service implements a very simple REST style API. This package make
requests by the HTTP protocol to retreive the data. Hence, fast Internet
The web service implements a very simple REST-style API. This package makes
requests by the HTTP protocol to retrieve the data. Hence, fast Internet
access is required for a proper use of *OmnipathR*.

#### What is OmniPath?
Expand Down Expand Up @@ -50,23 +50,23 @@ TF census, TRRUST and Vinayagam et al. 2011.

The latest version of the reference manual is available from
<https://static.omnipathdb.org/omnipathr_manual.pdf>. Tutorials can be
found at <https://workflows.omnipathdb.org/>. Sroll down for quick start
found at <https://workflows.omnipathdb.org/>. Scroll down for quick start
examples.

## OmniPath query types

We provide here a brief summary about the data available through *OmnipathR*.
We provide here a brief summary of the data available through *OmnipathR*.
*OmnipathR* provides access to 5 types of queries:

1. **Interactions**: protein-protein interactions from different datasets.
2. **Enzyme-substrate**: enzyme-PTM (post-translational modification)
relationships.
3. **Complexes**: comprehensive database of more than 22000 protein complexes.
4. **Annotations**: large variety of data about proteins and complexes
4. **Annotations**: large variety of data about protein and complex
features.
5. **Intercell**: information on the roles in inter-cellular signaling.

For a more detailed information, we recommend you to visit the following
For more detailed information, we recommend you to visit the following
sites:

<https://omnipathdb.org/>
Expand Down Expand Up @@ -95,7 +95,7 @@ if (!requireNamespace('BiocManager', quietly = TRUE))
## Last release in Bioconductor
BiocManager::install('OmnipathR', version = '3.12')
## Development version with the lastest updates
## Development version with the latest updates
BiocManager::install('OmnipathR', version = 'devel')
```

Expand Down Expand Up @@ -173,7 +173,7 @@ print_interactions(dplyr::filter(enzsub,enzyme_genesymbol=='MAP2K1',
```

Find shortest paths on the directed network between proteins:
Find the shortest paths on the directed network between proteins:
```{r}
print_path_es(shortest_paths(OPI_g,from = 'TYRO3',to = 'STAT3',
output = 'epath')$epath[[1]],OPI_g)
Expand Down Expand Up @@ -227,11 +227,11 @@ use pypath if you want to:
protein sequences, processing BioPAX, etc.

With *pypath* it's also possible to run your own web service and serve your
custom databases to the *OmnipathR* R client and the *omnipath* Python cient.
custom databases to the *OmnipathR* R client and the *omnipath* Python client.

## Feedbacks, bug reports, features

Feedbacks and bugreports are always very welcome!
Feedbacks and bug reports are always very welcome!

Please use the Github issue page to report bugs or for questions:

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