To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("blima")
In most cases, you don't need to download the package archive at all.
blima
Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
Bioconductor version: 3.1
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: Vojtech Kulvait
Maintainer: Vojtech Kulvait <kulvait at gmail.com>
Citation (from within R,
enter citation("blima")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("blima")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("blima")
| R Script | blima.pdf | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Microarray, Normalization, Preprocessing, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (1 year) |
| License | GPL-3 |
| Depends | R (>= 3.0.0) |
| Imports | beadarray(>= 2.0.0), Biobase(>= 2.0.0), BiocGenerics, grDevices, stats, graphics |
| LinkingTo | |
| Suggests | xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi |
| SystemRequirements | |
| Enhances | |
| URL | https://bitbucket.org/kulvait/blima |
| Depends On Me | |
| Imports Me | |
| Suggests Me | blimaTestingData |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | blima_1.2.0.tar.gz |
| Windows Binary | blima_1.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | blima_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | blima_1.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/blima/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/blima/ |
| Package Downloads Report | Download Stats |
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