blima
This package is for version 3.9 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: 3.9
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>
citation("blima")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| blima.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneRegulation, Microarray, Normalization, Preprocessing, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 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 |
| System Requirements | |
| URL | https://bitbucket.org/kulvait/blima |
See More
| Suggests | xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | blimaTestingData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | blima_1.18.0.tar.gz |
| Windows Binary | blima_1.18.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | blima_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/blima |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/blima |
| Bioc Package Browser | https://code.bioconductor.org/browse/blima/ |
| Package Short Url | https://bioconductor.org/packages/blima/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |