lgatto / pRoloc

A unifying bioinformatics framework for organelle proteomics
http://lgatto.github.io/pRoloc/
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bioconductor proteomics proteomics-data r spatial-proteomics visualisation

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A unifying bioinformatics framework for spatial proteomics

The pRoloc suite set of software offers a complete software pipeline to analyse, visualise and interpret mass spectrometry-based spatial proteomics data such, for example, as LOPIT (Localization of Organelle Proteins by Isotope Tagging), PCP (Protein Correlation Profiling) or hyperLOPIT (hyperplexed LOPIT). The suite includes pRoloc, the mail software that focuses on data analysis using state-of-the-art machine learning, pRolocdata, that distributes numerous datasets, and pRolocGUI, that offers interactive visualisations dedicated to spatial proteomics. The software are distributed as part of the R/Bioconductor project.

Getting started

The pRoloc software comes with ample documentation. The main tutorial provides a broad overview of the package and its functionality. See the Articles tab for additional manuals.

pRolocGUI also offer several documentation files.

Here are a set of video tutorial that illustrate the pRoloc framework.

Help

Post your questions on the Bioconductor support site, tagging it with the package name pRoloc (the maintainer will automatically be notified by email). If you identify a bug or have a feature request, please open an issue on the github development page.

Installation

The preferred installation procedure uses the Bioconductor infrastructure:

## unless BiocManager is already installed
install.packages("BiocManager")
## then
BiocManager::install("pRoloc")
BiocManager::install("pRolocdata")
BiocManager::install("pRolocGUI")

Pre-release/development version

The pre-release/development code on github can also be installed using BiocManager::install, as shown below. Note that this requires a working R build environment (i.e Rtools on Windows - see here). New pre-release features might not be documented not thoroughly tested and could substantially change prior to release. Use at your own risks.

## unless BiocManager is already installed
install.packages("BiocManager")
## then, install from github
BiocManager::install("lgatto/pRoloc")
BiocManager::install("lgatto/pRolocdata")
BiocManager::install("lgatto/pRolocGUI")

References:

For refences about the software, how to use it and spatial proteomics data analysis:

Specific algorithms available in the software:

More resource

Contributing

Contributions to the package are more than welcome. If you want to contribute to this package, you should follow the same conventions as the rest of the functions whenever it makes sense to do so. Feel free to get in touch (preferable opening a github issue) to discuss any suggestions.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.