{ "_id": "6a1ac0bf1d7bb097a09d715c", "Package": "PLSDAbatch", "Type": "Package", "Title": "PLSDA-batch", "Version": "2.1.0", "Authors@R": "c(person(given = \"Yiwen (Eva)\", family = \"Wang\", role = c(\"aut\", \"cre\"), email = \"anjiwangyiwen@gmail.com\", comment=c(ORCID=\"0000-0002-7067-9093\")),\nperson(given = \"Kim-Anh\", family = \"Le Cao\", role = \"aut\", email = \"kimanh.lecao@unimelb.edu.au\"))", "Description": "A novel framework to correct for batch effects prior to\nany downstream analysis in microbiome data based on Projection\nto Latent Structures Discriminant Analysis. The main method is\nnamed “PLSDA-batch”. It first estimates treatment and batch\nvariation with latent components, then subtracts\nbatch-associated components from the data whilst preserving\nbiological variation of interest. PLSDA-batch is highly\nsuitable for microbiome data as it is non-parametric,\nmultivariate and allows for ordination and data visualisation.\nCombined with centered log-ratio transformation for addressing\nuneven library sizes and compositional structure, PLSDA-batch\naddresses all characteristics of microbiome data that existing\ncorrection methods have ignored so far. Two other variants are\nproposed for 1/ unbalanced batch x treatment designs that are\ncommonly encountered in studies with small sample sizes, and\nfor 2/ selection of discriminative variables amongst treatment\ngroups to avoid overfitting in classification problems. These\ntwo variants have widened the scope of applicability of\nPLSDA-batch to different data settings.", "License": "GPL-3", "biocViews": "StatisticalMethod, DimensionReduction, PrincipalComponent,\nClassification, Microbiome, BatchEffect, Normalization,\nVisualization", "VignetteBuilder": "knitr", "RdMacros": "Rdpack", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "URL": "https://github.com/EvaYiwenWang/PLSDAbatch", "BugReports": "https://github.com/EvaYiwenWang/PLSDAbatch/issues/", "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nmake texlive libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:03 UTC", "RemoteUrl": "https://github.com/bioc/PLSDAbatch", "RemoteRef": "HEAD", "RemoteSha": "5f1e8350ea8ed96974ad5bc96ed0ee178ee57dd4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:17:41 UTC", "User": "root" }, "Author": "Yiwen (Eva) Wang [aut, 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