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Bioconductor - DaMiRseq (development version)

DaMiRseq

This is the development version of DaMiRseq; for the stable release version, see DaMiRseq.

Data Mining for RNA-seq data: normalization, feature selection and classification

Bioconductor version: Development (3.22)

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.

Author: Mattia Chiesa <mattia.chiesa at cardiologicomonzino.it>, Luca Piacentini <luca.piacentini at cardiologicomonzino.it>

Maintainer: Mattia Chiesa <mattia.chiesa at cardiologicomonzino.it>

Citation (from within R, enter citation("DaMiRseq")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DaMiRseq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DaMiRseq")
Data Mining for RNA-seq data: normalization, features selection and classification - DaMiRseq package PDF R Script Reference Manual PDF NEWS Text Details biocViews Classification, ImmunoOncology, RNASeq, Sequencing, Software Version 2.21.0 In Bioconductor since BioC 3.5 (R-3.4) (8 years) License GPL (>= 2) Depends R (>= 3.5.0), SummarizedExperiment, ggplot2 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 System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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