DaMiRseq

DOI: 10.18129/B9.bioc.DaMiRseq    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

PDF	R Script	Data Mining for RNA-seq data: normalization, features selection and classification - DaMiRseq package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, ImmunoOncology, RNASeq, Sequencing, Software
Version	2.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 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
LinkingTo
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	GARS
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	DaMiRseq_2.8.0.tar.gz
Windows Binary	DaMiRseq_2.8.0.zip
macOS Binary (x86_64)	DaMiRseq_2.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DaMiRseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DaMiRseq
Package Short Url	https://bioconductor.org/packages/DaMiRseq/
Package Downloads Report	Download Stats