Package: SerolyzeR 1.5.0

Jakub Grzywaczewski

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

Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project 'PvSTATEM', which is an international project aiming for malaria elimination.

Authors:Jakub Grzywaczewski [aut, cre], Tymoteusz Kwiecinski [aut], Mateusz Nizwantowski [aut], Przemyslaw Biecek [ths], Nuno Sepulveda [ths]

SerolyzeR_1.5.0.tar.gz
SerolyzeR_1.5.0.zip(r-4.7-any)SerolyzeR_1.5.0.zip(r-4.6-any)SerolyzeR_1.5.0.zip(r-4.5-any)
SerolyzeR_1.5.0.tgz(r-4.6-any)SerolyzeR_1.5.0.tgz(r-4.5-any)
SerolyzeR_1.5.0.tar.gz(r-4.7-any)SerolyzeR_1.5.0.tar.gz(r-4.6-any)
SerolyzeR_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SerolyzeR/json (API)

# Install 'SerolyzeR' in R:
install.packages('SerolyzeR', repos = c('https://mini-pw.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mini-pw/serolyzer/issues

Pkgdown/docs site:https://mini-pw.github.io

On CRAN:

Conda:

6.56 score 10 stars 10 scripts 292 downloads 24 exports 50 dependencies

Last updated from:fab7befefb. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK314
source / vignettesOK316
linux-releaseOK286
macos-releaseOK259
macos-oldrelOK203
windows-develOK215
windows-releaseOK184
windows-oldrelOK216
wasm-releaseOK146

Exports:create_standard_curve_model_analytedetect_mba_formatgenerate_levey_jennings_reportgenerate_plate_reportget_nmfiis_valid_data_typeis_valid_sample_typemerge_plate_outputsPlateBuilderplot_countsplot_layoutplot_levey_jenningsplot_mfi_for_analyteplot_standard_curve_analyteplot_standard_curve_analyte_with_modelplot_standard_curve_stackedprocess_dirprocess_fileprocess_plateread_layout_dataread_luminex_dataread_xponent_formatrun_guitranslate_sample_names_to_sample_types

Dependencies:base64enccellrangerclicpp11crayondplyrfarverfsgenericsggplot2ggrepelgluegtablehmsisobandjsonlitelabelinglifecyclelubridatemagrittrnplrpatchworkpillarpkgconfigpngprettyunitsprogressR.methodsS3R.ooR.utilsR6RColorBrewerRcppreadxlrematchrlangS7scalesstringistringrsvglitesystemfontstextshapingtibbletidyselecttimechangeutf8vctrsviridisLitewithr

Basic SerolyzeR functionalities
Reading the plate object | Processing the whole plate | Quality control and normalisation details | Plate summary and details | Quality control | Normalisation | RAU vs dilution | Inner nplr model | Predicting RAU | Usage | nMFI
Rendered fromexample_script.Rmdusingknitr::rmarkdown

Last update: 2026-01-17
Started: 2024-07-08

Multiplate SerolyzeR functionalities
Introduction | Reading the data | Reading a whole directory
Rendered frommultiplate_tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-01-17
Started: 2025-03-16

Our datasets
Introduction | How to access the files | Description of the datasets | Artificial datasets | Public datasets | External datasets
Rendered fromour_datasets.Rmdusingknitr::rmarkdown

Last update: 2026-01-17
Started: 2024-07-17

Raw data parsers
Introduction | Basic data loading | SerolyzeR as an MBA data reader
Rendered fromparsers.Rmdusingknitr::rmarkdown

Last update: 2026-01-17
Started: 2025-01-03

SerolyzeR HTML reports
Introduction | Plate summary report | Generating the report | Warnings | Additional parameters | Levey-Jennings report
Rendered fromour_reports.Rmdusingknitr::rmarkdown

Last update: 2025-07-16
Started: 2025-01-03

SerolyzeR plots
Introduction | Plate layout | Counts for a given analyte | Distribution of MFI values | Standard curve plots | Standard curve plot without model | Standard curve plot with model | Standard curve plot stacked | Levey-Jennings plot
Rendered fromour_plots.Rmdusingknitr::rmarkdown

Last update: 2025-07-09
Started: 2024-08-27

Readme and manuals

Help Manual

Help pageTopics
Create a standard curve model for a certain analytecreate_standard_curve_model_analyte
Try to detect the format of a filedetect_mba_format
Generate a Levey-Jennings Report for Multiple Plates.generate_levey_jennings_report
Generate a report for a plate.generate_plate_report
Calculate Normalised MFI (nMFI) Values for a Plateget_nmfi
Detect and handle the high dose hook effecthandle_high_dose_hook
Check validity of given data typeis_valid_data_type
Check validity of given sample typeis_valid_sample_type
Merge Normalised Data from Multiple Platesmerge_plate_outputs
Logistic regression model for the standard curveModel
Plate ObjectPlate
PlateBuilderPlateBuilder
Plot counts in a 96-well plateplot_counts
Plot layout of a 96-well plateplot_layout
Plot Levey-Jennings chartplot_levey_jennings
Plot MFI value distribution for a given analyteplot_mfi_for_analyte
Standard curvesplot_standard_curve_analyte
Plot standard curve of a certain analyte with fitted modelplot_standard_curve_analyte_with_model
Standard curve stacked plot for levey-jennings reportplot_standard_curve_stacked
Predict the RAU values from the MFI valuespredict.Model
Process a Directory of Luminex Data Filesprocess_dir
Process a File to Generate Normalised Data and Reportsprocess_file
Process Plate Data and Save Normalised Outputprocess_plate
Read the BIOPLEX format dataread_bioplex_format
Read the Intelliflex format dataread_intelliflex_format
Read layout data from a fileread_layout_data
Read Luminex Dataread_luminex_data
Read the xPONENT format dataread_xponent_format
Launch the interactive GUI Shiny apprun_gui
Translate sample names to sample typestranslate_sample_names_to_sample_types