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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
affypdnn Laurent Gautier Probe Dependent Nearest Neighbours (PDNN) for the affy package
affyPLM Ben Bolstad Methods for fitting probe-level models
affyQCReport Craig Parman QC Report Generation for affyBatch objects
altcdfenvs Laurent Gautier alternative cdfenvs
annaffy Colin A. Smith Annotation tools for Affymetrix biological metadata
aroma.light Henrik Bengtsson Light-weight methods for normalization and visualization of microarray data using only basic R data types
beadarray Mark Dunning Quality control and low-level analysis of BeadArrays
BeadExplorer Gareth Elvidge QC, normalisation, annotation and exploration of Illumina BeadChip data
bridge Raphael Gottardo Bayesian Robust Inference for Differential Gene Expression
codelink Diego Diez Manipulation of Codelink Bioarrays data.
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
exonmap Crispin Miller High level analysis of Affymetrix exon array data
gcrma Z. Wu Background Adjustment Using Sequence Information
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
GlobalAncova R. Meister Calculates a global test for differential gene expression between groups
globaltest Jelle Goeman Testing Association of Groups of Genes with a Clinical Variable
lapmix Yann Ruffieux Laplace Mixture Model in Microarray Experiments
limma Gordon Smyth Linear Models for Microarray Data
lumi Pan Du BeadArray Specific Methods for Illumina Microarrays
maDB Johannes Rainer Microarray database and utility functions for microarray data analysis.
makecdfenv James W. MacDonald CDF Environment Maker
makePlatformDesign Benilton Carvalho Platform Design Package
oligo Benilton Carvalho Oligonucleotide Arrays
oneChannelGUI Raffaele A Calogero This package extends the capabilities of affylmGUI graphical interface.
puma Richard Pearson Propagating Uncertainty in Microarray Analysis
RefPlus Kai-Ming Chang A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays
SAGx Per Broberg Statistical Analysis of the GeneChip
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
tilingArray W. Huber Analysis of high-density oligonucleotide tiling arrays
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
webbioc Colin A. Smith Bioconductor Web Interface