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Package Maintainer Title
ABarray Yongming Andrew Sun Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data.
affy Rafael A. Irizarry Methods for Affymetrix Oligonucleotide Arrays
affycomp Rafael A. Irizarry Graphics Toolbox for Assessment of Affymetrix Expression Measures
affycoretools James W. MacDonald Functions useful for those doing repetitive analyses with Affymetrix GeneChips.
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
affylmGUI Keith Satterley GUI for affy analysis using limma package
affyPara Markus Schmidberger Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
affypdnn Laurent Gautier Probe Dependent Nearest Neighbours (PDNN) for the affy package
affyPLM Ben Bolstad Methods for fitting probe-level models
Agi4x44PreProcess Pedro Lopez-Romero PreProcessing of Agilent 4x44 array data
altcdfenvs Laurent Gautier alternative CDF environments (aka mappings)
aroma.light Henrik Bengtsson Light-weight methods for normalization and visualization of microarray data using only basic R data types
ArrayTools Arthur Li geneChip Analysis Package
beadarray Mark Dunning Quality assessment and low-level analysis for Illumina BeadArray data
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
CALIB Hui Zhao Calibration model for estimating absolute expression levels from microarray data
CGHcall Sjoerd Vosse Calling aberrations for array CGH tumor profiles.
codelink Diego Diez Manipulation of Codelink Bioarrays data.
exonmap Crispin Miller High level analysis of Affymetrix exon array data
gcrma Z. Wu Background Adjustment Using Sequence Information
genArise IFC Development Team Microarray Analysis tool
HELP Reid F. Thompson Tools for HELP data analysis
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Keith Satterley GUI for limma package
LMGene John Tillinghast LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
lumi Pan Du BeadArray Specific Methods for Illumina Microarrays
maCorrPlot Alexander Ploner Visualize artificial correlation in microarray data
maigesPack Gustavo H. Esteves Functions to handle cDNA microarray data, including several methods of data analysis
makecdfenv James W. MacDonald CDF Environment Maker
makePlatformDesign Benilton Carvalho Platform Design Package
MANOR Pierre Neuvial CGH Micro-Array NORmalization
marray Yee Hwa (Jean) Yang Exploratory analysis for two-color spotted microarray data
multiscan Mizanur Khondoker R package for combining multiple scans
nnNorm Adi Laurentiu Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
oligo Benilton Carvalho Oligonucleotide Arrays
OLIN Matthias Futschik Optimized local intensity-dependent normalisation of two-color microarrays
OLINgui Matthias Futschik Graphical user interface for OLIN
oneChannelGUI Raffaele A Calogero This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files.
puma Richard Pearson Propagating Uncertainty in Microarray Analysis
rama Raphael Gottardo Robust Analysis of MicroArrays
RefPlus Kai-Ming Chang A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
Ringo J. Toedling R Investigation of ChIP-chip Oligoarrays
RNAither Nora Rieber Statistical analysis of high-throughput RNAi screens
SAGx Per Broberg, Statistical Analysis of the GeneChip
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
snapCGH Thomas Hardcastle Segmentation, normalisation and processing of aCGH data.
spotSegmentation Chris Fraley Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
stepNorm Yuanyuan Xiao Stepwise normalization functions for cDNA microarrays
tilingArray W. Huber Analysis of high-density oligonucleotide tiling arrays
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
xps Christian Stratowa Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays