Package: wpm 1.15.0

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]

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wpm.pdf |wpm.html✨
wpm/json (API)
NEWS

# 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-1.15.0(bioc 3.20)wpm-1.14.0(bioc 3.19)

bioconductor-package

7 exports 0.49 score 100 dependencies

Last updated 2 months agofrom:761777a711

Exports:convertCSV convertESet convertSE convertVector2Df drawMap wpm wrapperWPM

Dependencies:abind anytime askpass attempt base64enc BH Biobase BiocGenerics bslib cachem cli colorspace commonmark config crayon crosstalk curl DelayedArray digest dplyr DT evaluate fansi farver fastmap fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue golem gtable here highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle logging magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig promises R6 rappdirs RColorBrewer Rcpp rlang rmarkdown rprojroot S4Arrays S4Vectors sass scales shiny shinycustomloader shinydashboard shinyWidgets sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun xtable XVector yaml zlibbioc

How to use Well Plate Maker

Helene Borges

Rendered fromwpm_vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

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 1.15.0

wpm: Well Plate Maker

How to use Well Plate Maker

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)