IMPORTANT: THIS IS ACTIVELY DEVELOPED.
RuSirius is an R package that provides an interface to the Sirius software,
enabling seamless integration of xcms preprocessing results with Sirius.
It is built upon Rsirius, the REST API library for the R programming
language, which you can find
here.
- You can install both the Sirius software and the R API using conda with the following command:
conda install conda-forge::r-sirius-ms- Then install RuSirius and it's dependencies :
library(remotes)
BiocManager::install("RforMassSpectrometry/RuSirius")Alternatively, you can manually install Sirius and then RuSirius:
- Download the Sirius software from the official releases page. RuSirius is dependent on Sirius 6.1, please ensure you have the right version downloaded.
- Install RuSirius and it's dependencies (which includes the R-api) by running the following code in R:
library(remotes)
BiocManager::install("RforMassSpectrometry/RuSirius")Lastly, please install the devel version of xcms (this is temporary and will not be needed after the next bioconductor release.)
BiocManager::install("sneumann/xcms", ref = "devel")RuSirius comes with two vignettes to help you get started:
-
Importing Chromatographic Peaks from xcms
This vignette demonstrates how to import chromatographic peaks from xcms and use them in Sirius. -
Importing Features from xcms
This vignette shows how to import features (i.e., corresponding chromatographic peaks) from xcms and use them in Sirius.
Note: The second vignette is not fully reproducible yet, as the dataset used is not publicly available. However, the code can serve as a template for your use case. A public dataset will be added soon.
We’re looking for testers to help refine and enhance the functionality of this package, focusing on what users need most. Your feedback is crucial to ensuring the package meets user expectations and operates smoothly.
-
Ease of Installation
Start by testing the installation process. Let us know if you encounter any issues, especially with package dependencies. -
Exploring Basic Functionalities
Run the first vignette suggested above to familiarize yourself with the package’s core features. This will give you a solid foundation for understanding how it works. -
Adapting to Your Dataset
If you’re working with custom datasets or want to import features instead of chromatographic peaks, try the second vignette. It provides the necessary code and steps for more advanced use cases.
The current implementation is in its early stages, focusing on basic functionality. Your input is essential to making the integration between xcms and Sirius seamless and user-friendly. Whether you have suggestions, encounter issues, or need additional features, don’t hesitate to reach out. Your insights will directly shape future updates.
This is the early stage of integrating Sirius with RforMassSpectrometry, and there’s ongoing development to enhance the implementation.
-
GHA and R command checks: They are failing/incomplete because the vignettes cannot be run systematically for now. The logIn system is blocking this at the moment. But working on it.
-
Docker image: a DockerFile is available, however the vignettes cannot be run on it yet. It's a work in progress, Sirius cannot be started properly.
-
Importing features can be time-consuming. To speed up testing, import only a few features at first and limit the process to one MS1 spectrum per feature. Further details are provided in the vignettes.
If you encounter other issues, please let us know so we can improve the package!
Many many thanks to Markus Fleischauer for his work on the Sirius SDKs, many more Jonas Emmert who made the R-API usable. And Marcus Ludwig for the help and support in implementing RuSirius.