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NAMESPACE 100644 1 kb
NEWS.md 100644 1 kb
README.md 100644 3 kb
README.md
<!-- PLEASE DO NOT EDIT ./README.md BY HAND, EDIT ./inst/README.Rmd AND RENDER TO CREATE ./README.md --> [![](https://img.shields.io/github/last-commit/EvaYiwenWang/PLSDAbatch.svg)](https://github.com/EvaYiwenWang/PLSDAbatch/commits/master) [![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3) [![](https://img.shields.io/github/languages/code-size/EvaYiwenWang/PLSDAbatch.svg)](https://github.com/EvaYiwenWang/PLSDAbatch) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) # PLSDAbatch A multivariate and non-parametric batch effect correction framework based on Projection to Latent Structures Discriminant Analysis for microbiome data. This repository contains the `R` package hosted on Bioconductor. ## Maintainer [Yiwen (Eva) Wang](mailto:wangyiwen@caas.cn) ## Installation (**macOS users only:** Ensure you have installed [XQuartz](https://www.xquartz.org/) first.) Make sure you have the latest R version and the latest `BiocManager` package installed following [these instructions](https://www.bioconductor.org/install/). ``` r ## install BiocManager if not installed if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") ``` Ensure the following returns `TRUE`, or follow the guidelines provided by the output. ``` r BiocManager::valid() ``` #### a) Latest `Bioconductor` Release (not now, wait for Bioconductor release) You can install `PLSDAbatch` using the following code: ``` r BiocManager::install('PLSDAbatch') ``` #### b) `GitHub` Version Install the GitHub version with: ``` r # without vignette BiocManager::install("EvaYiwenWang/PLSDAbatch") # with vignette devtools::install_github("https://github.com/EvaYiwenWang/PLSDAbatch", build_vignettes = T) ``` ## Functions preview ``` r library(PLSDAbatch) ## names ls('package:PLSDAbatch') ## names and details lsf.str('package:PLSDAbatch') ``` ## Vignette View ``` r browseVignettes("PLSDAbatch") ``` ## Bug reports/Feature requests [Open a new issue](https://github.com/EvaYiwenWang/PLSDAbatch/issues). ## Reference Wang, Y., & Lê Cao, K. A. (2023). PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data. Briefings in Bioinformatics, 24(2), bbac622. <https://academic.oup.com/bib/article/24/2/bbac622/6991121> (The mentioned simulations and analyses in the paper are separately stored [here](https://evayiwenwang.github.io/PLSDAbatch_workflow/).) ## What’s New #### April 2023 - submitted to Bioconductor. #### September 2024 - fixed bugs: the clash of functions from dependencies.