Package: DaMiRseq Type: Package Date: 2021-11-20 Title: Data Mining for RNA-seq data: normalization, feature selection and classification Version: 2.25.0 Author: Mattia Chiesa , Luca Piacentini Maintainer: Mattia Chiesa Description: The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes. The package accepts any kind of data presented as a table of raw counts and allows including both continous and factorial variables that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e. batches and confounding factors) and to select the best predictors for modeling. Finally, a "stacking" ensemble learning technique is applied to build a robust classification model. Every step includes a checkpoint that the user may exploit to assess the effects of data management by looking at diagnostic plots, such as clustering and heatmaps, RLE boxplots, MDS or correlation plot. License: GPL (>= 2) Encoding: UTF-8 LazyData: true biocViews: Sequencing, RNASeq, Classification, ImmunoOncology VignetteBuilder: knitr Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr, Seqinfo Suggests: BiocStyle, knitr, testthat Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 RoxygenNote: 7.1.1 Config/pak/sysreqs: cmake libfreetype6-dev libglpk-dev make default-jdk libbz2-dev libicu-dev libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:45:17 UTC RemoteUrl: https://github.com/bioc/DaMiRseq RemoteRef: HEAD RemoteSha: 89e0c2e4158c20e33904ef5495f0d9e5fc3dc8fe NeedsCompilation: no Packaged: 2026-07-05 14:04:49 UTC; root