Package: wpm 1.23.0

Helene Borges

wpm: Well Plate Maker

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.

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

wpm_1.23.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
wpm/json (API)

# Install 'wpm' in R:

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

Bug tracker:https://github.com/helbor/wpm/issues

Datasets:

data_test - Fictitious clinical data for demonstration.

On BioConductor:wpm-1.23.0(bioc 3.24)wpm-1.22.0(bioc 3.23)

gui proteomics massspectrometry batcheffect experimentaldesign

4.78 score 6 stars 8 scripts 7 exports 85 dependencies

Last updated from:46b4d1a203. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	173
linux-devel-x86_64	NOTE	222
source / vignettes	OK	244
linux-release-x86_64	NOTE	268
macos-release-arm64	NOTE	109
macos-oldrel-arm64	NOTE	104
windows-devel	NOTE	117
windows-release	NOTE	147
windows-oldrel	NOTE	159
wasm-release	OK	174

Exports:convertCSV convertESet convertSE convertVector2Df drawMap wpm wrapperWPM

Dependencies:abind attempt base64enc Biobase BiocGenerics bslib cachem cli codetools commonmark config cpp11 crosstalk DelayedArray digest dplyr DT evaluate farver fastmap fontawesome fs generics GenomicRanges ggplot2 glue golem gtable highr htmltools htmlwidgets httpuv IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle logging magrittr Matrix MatrixGenerics matrixStats memoise mime otel pillar pkgconfig promises R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo shiny shinycustomloader shinydashboard shinyWidgets sourcetools SparseArray stringi stringr SummarizedExperiment tibble tidyselect tinytex utf8 vctrs viridisLite withr xfun xtable XVector yaml

How to use Well Plate Maker

Rendered fromwpm_vignette.Rmdusingknitr::rmarkdown

Last update: 2021-03-17
Started: 2020-04-29

Help page	Topics
Backtracking Function	backtracking
Makes a balanced distribution of the elements between several plates.	balancedGrpDistrib
Check for spatial constraints	checkConstraints
Check the inputs for the wrapper function	checkWpmInputs
Convert a CSV File into a valid dataframe for WPM	convertCSV
Convert the phenotype data of an ExpressionSet or MsnSet into a dataframe for WPM	convertESet
Convert the phenotype data of a SummarizedExperiment into a dataframe for WPM	convertSE
Convert a vector of plate coordinates into a dataframe	convertVector2Df
Fictitious clinical data for demonstration.	data_test
Determines buffer wells coordinates on a plate	defineBufferCoords
Generate a ggplot object of a plate plan	drawMap
Find the 4 cardinal neighbors of an element of a matrix	findNEWSneighbors
Find the top and bottom neighbors of an element of a matrix	findNSneighbors
Find the left and right neighbors of an element of a matrix	findWEneighbors
Generate a plate map according to the input parameters	generateMap
Binds multiple dataframes together	joinDataframes
Random walk of the matrix to fill	randomWalk
Randomly take a number of elements in a vector	resample
Affects a sample to the chosen cell in the plate	solveCell
Run the Shiny Application of Well Plate Maker	wpm
Generate plate plans in a single step	wrapperWPM

Package: wpm 1.23.0

wpm: Well Plate Maker

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Usage by other packages (reverse dependencies)