diff --git a/README.md b/README.md index b123a64..969a448 100644 --- a/README.md +++ b/README.md @@ -19,8 +19,8 @@ An `R` client for the **OmniPath** web service and many other resources. -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? @@ -50,23 +50,23 @@ TF census, TRRUST and Vinayagam et al. 2011. The latest version of the reference manual is available from . Tutorials can be -found at . Sroll down for quick start +found at . 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: @@ -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') ``` @@ -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) @@ -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: