Package: DaMiRseq
Type: Package
Date: 2021-11-20
Title: Data Mining for RNA-seq data: normalization, feature selection
        and classification
Version: 2.23.0
Author: Mattia Chiesa <mattia.chiesa@cardiologicomonzino.it>, Luca
        Piacentini <luca.piacentini@cardiologicomonzino.it>
Maintainer: Mattia Chiesa <mattia.chiesa@cardiologicomonzino.it>
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
Suggests: BiocStyle, knitr, testthat
Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2
RoxygenNote: 7.1.1
Config/pak/sysreqs: cmake libglpk-dev make default-jdk libbz2-dev
        libicu-dev libjpeg-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:37:23 UTC
RemoteUrl: https://github.com/bioc/DaMiRseq
RemoteRef: HEAD
RemoteSha: 48f9b25f435691e03b406fc98ab7af253f297d25
NeedsCompilation: no
Packaged: 2026-02-08 09:33:45 UTC; root
Built: R 4.6.0; ; 2026-02-08 09:36:45 UTC; windows
