To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DaMiRseq")

In most cases, you don't need to download the package archive at all.

DaMiRseq

 

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

Bioconductor version: Release (3.5)

The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for classification purposes.. The package accepts any kind of data presented as a table of raw counts and allows including covariates 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 hotmail.it>, Luca Piacentini <luca.piacentini at cardiologicomonzino.it>

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DaMiRseq")

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
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, RNASeq, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL (>= 2)
Depends R (>= 3.4), 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
LinkingTo
Suggests BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source DaMiRseq_1.0.0.tar.gz
Windows Binary DaMiRseq_1.0.0.zip
Mac OS X 10.11 (El Capitan) DaMiRseq_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DaMiRseq
Package Short Url http://bioconductor.org/packages/DaMiRseq/
Package Downloads Report Download Stats

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