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SerolyzeR

R package for automated analysis of serological data

https://github.com/mini-pw/SerolyzeR

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (20.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

R package for automated analysis of serological data

Basic Info
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 2
  • Open Issues: 8
  • Releases: 0
Created almost 2 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.md

SerolyzeR - an R package for automated analysis of serological data

R-CMD-check Downloads codecov <!-- badges: end -->

Overview

This package is a simple tool that handles various raw data formats produced in Multiplex Bead Assay (MBA). In short, it reads the unstructured, raw data from, e.g., the Luminex device and outputs normalised and well-structured data, which can be used later in more advanced downstream analysis.

The package includes three main steps for preprocessing the data:

  1. data reading and manipulation
  2. quality control
  3. data normalisation

The graphical overview of the package can be seen in the image below:

overview

SerolyzeR package is developed within the PvSTATEM initiative. The project has received funding from the European Union’s Horizon Europe research and innovation program under grant agreement No 101057665.

Previously, this package was named PvSTATEM, but it has been rebranded to SerolyzeR to better reflect its purpose and scope.

Installation

The easiest way to install the package is using the CRAN repository: r install.packages("SerolyzeR") require(SerolyzeR) # load the installed package Now, you are ready to use the package to read your files!

Please note that since uploading the package to the CRAN repository requires the volunteers' time to manually run checks on the packages, the package version currently released on CRAN might not be the latest.

The package is under heavy development, with new features being released weekly. Therefore, if you'd like to test the latest package functionalities, we recommend installing it in the development version. It can be done using a simple command install_github available in the devtools library:

r require(devtools) install_github("mini-pw/SerolyzeR") require(SerolyzeR) # load the installed package

The first command loads the devtools library (you might need to install it first - using the command install_packages("devtools")), and the second one sources the git repository with the code of our package and automatically installs it.

Examples and instructions

The example use of the package and its functionalities can be found in the vignettes. For more detailed documentation, check the package website.

Contributing and issues

As a project in the development phase, we are open to any suggestions, bug reports, and contributions. If you have any ideas or issues, please report them in the Issues section. Our team of developers will address them as soon as possible.

Acknowledgements

Funded by the European Union. Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or HaDEA. Neither the European Union nor the granting authority can be held responsible for them.

The package was developed as a Bachelor's thesis by Jakub Grzywaczewski, Tymoteusz Kwieciński and Mateusz Nizwantowski on Warsaw University of Technology, Faculty of Mathematics and Information Science, supervised by prof. dr hab. inż. Przemysław Biecek.



Owner

  • Name: MiNI PW
  • Login: mini-pw
  • Kind: organization

Faculty of Mathematics and Information Science at Warsaw University of Technology

GitHub Events

Total
  • Create event: 26
  • Release event: 1
  • Issues event: 40
  • Watch event: 7
  • Delete event: 23
  • Issue comment event: 50
  • Push event: 125
  • Pull request review comment event: 6
  • Pull request review event: 36
  • Pull request event: 56
  • Fork event: 2
Last Year
  • Create event: 26
  • Release event: 1
  • Issues event: 40
  • Watch event: 7
  • Delete event: 23
  • Issue comment event: 50
  • Push event: 125
  • Pull request review comment event: 6
  • Pull request review event: 36
  • Pull request event: 56
  • Fork event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 28
  • Total pull requests: 34
  • Average time to close issues: 20 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.32
  • Average comments per pull request: 0.97
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 28
  • Pull requests: 34
  • Average time to close issues: 20 days
  • Average time to close pull requests: 1 day
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.32
  • Average comments per pull request: 0.97
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Fersoil (27)
  • ZetrextJG (1)
Pull Request Authors
  • Fersoil (25)
  • ZetrextJG (5)
  • nizwant (4)
Top Labels
Issue Labels
documentation (2) wontfix (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 221 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: SerolyzeR

Reading, Quality Control and Preprocessing of MBA (Multiplex Bead Assay) Data

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 221 Last month
Rankings
Dependent packages count: 27.0%
Dependent repos count: 33.3%
Average: 49.1%
Downloads: 87.0%
Maintainers (1)
tymoteuszkwiecinski@gmail.com
Last synced: 10 months ago

Dependencies

.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.5.0 composite
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  • r-lib/actions/setup-pandoc v2 composite
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DESCRIPTION cran
  • R6 * imports
  • RColorBrewer * imports
  • dplyr * imports
  • readxl * imports
  • tools * imports
  • testthat >= 3.0.0 suggests
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.github/workflows/lint.yaml actions
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.github/workflows/style.yaml actions
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.github/workflows/test-coverage.yaml actions
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.github/workflows/roxygenize.yaml actions
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