blima

DOI: 10.18129/B9.bioc.blima    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see blima.

Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Bioconductor version: 3.12

Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

Author: Vojtěch Kulvait

Maintainer: Vojtěch Kulvait <kulvait at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("blima")

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("blima")

 

PDF	R Script	blima.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GeneRegulation, Microarray, Normalization, Preprocessing, Software
Version	1.24.0
In Bioconductor since	BioC 3.0 (R-3.1) (6.5 years)
License	GPL-3
Depends	R (>= 3.3)
Imports	beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics
LinkingTo	Rcpp
Suggests	xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr
SystemRequirements
Enhances
URL	https://bitbucket.org/kulvait/blima
Depends On Me
Imports Me
Suggests Me	blimaTestingData
Links To Me
Build Report

Package Archives

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

Source Package	blima_1.24.0.tar.gz
Windows Binary	blima_1.24.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	blima_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/blima
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/blima
Package Short Url	https://bioconductor.org/packages/blima/
Package Downloads Report	Download Stats