Package: PvSTATEM 0.1.2

Tymoteusz Kwiecinski

PvSTATEM: 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 of the same name - 'PvSTATEM', which is an international project aiming for malaria elimination.

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

PvSTATEM_0.1.2.tar.gz
PvSTATEM_0.1.2.tar.gz(r-4.5-noble)PvSTATEM_0.1.2.tar.gz(r-4.4-noble)
PvSTATEM_0.1.2.tgz(r-4.4-emscripten)PvSTATEM_0.1.2.tgz(r-4.3-emscripten)
PvSTATEM.pdf |PvSTATEM.html✨
PvSTATEM/json (API)

# Install 'PvSTATEM' in R:

install.packages('PvSTATEM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

3.18 score 2 scripts 530 downloads 14 exports 58 dependencies

Last updated 13 days agofrom:0b47c201ce. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 09 2024
R-4.5-linux	OK	Nov 09 2024

Exports:create_standard_curve_model_analyte generate_plate_report get_nmfi is_valid_data_type is_valid_sample_type PlateBuilder plot_counts plot_layout plot_mfi_for_analyte plot_standard_curve_analyte plot_standard_curve_analyte_with_model process_plate read_luminex_data translate_sample_names_to_sample_types

Dependencies:bit bit64 cellranger cli clipr colorspace cpp11 crayon dplyr fansi farver generics ggplot2 ggrepel glue gtable hms isoband labeling lattice lifecycle lubridate magrittr MASS Matrix mgcv munsell nlme nplr pillar pkgconfig png prettyunits progress R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp readr readxl rematch rlang scales stringi stringr svglite systemfonts tibble tidyselect timechange tzdb utf8 vctrs viridisLite vroom withr

Basic PvSTATEM functionalities

Tymoteusz Kwieciński

Rendered fromexample_script.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2024-11-02
Started: 2024-10-04

Help page	Topics
Create a standard curve model for a certain analyte	create_standard_curve_model_analyte
Generate a report for a plate.	generate_plate_report
Calculate normalised MFI values for a plate	get_nmfi
Detect and handle the high dose hook effect	handle_high_dose_hook
Check validity of given data type	is_valid_data_type
Check validity of given sample type	is_valid_sample_type
Logistic regression model for the standard curve	Model
Plate object	Plate
PlateBuilder	PlateBuilder
Plot counts in a 96-well plate	plot_counts
Plot layout of a 96-well plate	plot_layout
Plot MFI value distribution for a given analyte	plot_mfi_for_analyte
Standard curves	plot_standard_curve_analyte
Plot standard curve of a certain analyte with fitted model	plot_standard_curve_analyte_with_model
Predict the RAU values from the MFI values	predict.Model
Process a plate and save output values to a CSV	process_plate
Read the Intelliflex format data	read_intelliflex_format
Read layout data from a file	read_layout_data
Read Luminex Data	read_luminex_data
Read the xPONENT format data	read_xponent_format
Translate sample names to sample types	translate_sample_names_to_sample_types

Package: PvSTATEM 0.1.2

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

Basic PvSTATEM functionalities

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)