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Well Plate Maker

Bioconductor version: Release (3.19)

The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of batch effects. In particular, it helps controlling the "plate effect" thanks to its ability to randomize samples over multiple well plates. The algorithm for placing the samples is inspired by the backtracking algorithm: the samples are placed at random while respecting specific spatial constraints.

Author: Helene Borges [aut, cre], Thomas Burger [aut]

Maintainer: Helene Borges <borges.helene.sophie at>

Citation (from within R, enter citation("wpm")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

How to use Well Plate Maker HTML R Script
Reference Manual PDF


biocViews BatchEffect, ExperimentalDesign, GUI, MassSpectrometry, Proteomics, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.1.0)
Imports utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging
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Suggests MSnbase, testthat, BiocStyle, knitr, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package wpm_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) wpm_1.14.0.tgz
macOS Binary (arm64) wpm_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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