Bioconductor Task View: Microarray

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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.
aCGH Jane Fridlyand Classes and functions for Array Comparative Genomic Hybridization data.
adSplit Claudio Lottaz Annotation-Driven Clustering
affxparser Kasper Daniel Hansen Affymetrix File Parsing SDK
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
affyio Benjamin Milo Bolstad Tools for parsing Affymetrix data files
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
AnnBuilder J. Zhang Bioconductor annotation data package builder
annotationTools Alexandre Kuhn Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
aroma.light Henrik Bengtsson Light-weight methods for normalization and visualization of microarray data using only basic R data types
arrayMagic Andreas Buness two-colour cDNA array quality control and preprocessing
arrayQuality Agnes Paquet Assessing array quality on spotted arrays
arrayQualityMetrics Audrey Kauffmann Quality metrics on ExpressionSets
beadarray Mark Dunning Quality control and low-level analysis of BeadArrays
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
BeadExplorer Gareth Elvidge QC, normalisation, annotation and exploration of Illumina BeadChip data
bgx Ernest Turro Bayesian Gene eXpression
bridge Raphael Gottardo Bayesian Robust Inference for Differential Gene Expression
CALIB Hui Zhao Calibration model for estimating absolute expression levels from microarray data
cellHTS Ligia Bras Analysis of cell-based screens
cellHTS2 Ligia Bras Analysis of cell-based screens - revised version of cellHTS
CGHcall Sjoerd Vosse Calling aberrations for array CGH tumor profiles.
cghMCR J. Zhang Find chromosome regions showing common gains/losses
ChromoViz Jihoon Kim Multimodal visualization of gene expression data
codelink Diego Diez Manipulation of Codelink Bioarrays data.
convert Yee Hwa (Jean) Yang Convert Microarray Data Objects
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
CORREP Dongxiao Zhu Multivariate Correlation Estimator and Statistical Inference Procedures.
ctc Antoine Lucas Cluster and Tree Conversion.
daMA Jobst Landgrebe Efficient design and analysis of factorial two-colour microarray data
DEDS Yuanyuan Xiao Differential Expression via Distance Summary for Microarray Data
diffGeneAnalysis Choudary Jagarlamudi Performs differential gene expression Analysis
DNAcopy Venkatraman E. Seshan DNA copy number data analysis
exonmap Crispin Miller High level analysis of Affymetrix exon array data
explorase Michael Lawrence GUI for exploratory data analysis of systems biology data
factDesign Denise Scholtens Factorial designed microarray experiment analysis
fdrame Effi Kenigsberg FDR adjustments of Microarray Experiments (FDR-AME)
gcrma Z. Wu Background Adjustment Using Sequence Information
genArise IFC Development Team Microarray Analysis tool
genefilter Biocore Team c/o BioC user list genefilter: methods for filtering genes from microarray experiments
geneRecommender Greg Hather A gene recommender algorithm to identify genes coexpressed with a query set of genes
GeneTraffic Daniel Iordan GeneTraffic R Integration Functions
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
GGtools Vince Carey software and data for genetical genomics (c) 2006 VJ Carey
GLAD Philippe Hupe Gain and Loss Analysis of DNA
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
goTools Agnes Paquet Functions for Gene Ontology database
gpls Biocore Team c/o BioC user list Classification using generalized partial least squares
Heatplus Alexander Ploner A heat map displaying covariates and coloring clusters
HEM HyungJun Cho Heterogeneous error model for identification of differentially expressed genes under multiple conditions
impute Balasubramanian Narasimhan impute: Imputation for microarray data
lapmix Yann Ruffieux Laplace Mixture Model in Microarray Experiments
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
logicFS Holger Schwender Identification of SNP Interactions
LPE Nitin Jain Methods for analyzing microarray data using Local Pooled Error (LPE) method
lumi Pan Du BeadArray Specific Methods for Illumina Microarrays
maanova Hyuna Yang Tools for analyzing Micro Array experiments
macat Joern Toedling MicroArray Chromosome Analysis Tool
maCorrPlot Alexander Ploner Visualize artificial correlation in microarray data
maDB Johannes Rainer Microarray database and utility functions for microarray data analysis.
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
maSigPro Ana Conesa Significant Gene Expression Profile Differeneces in Time Course Microarray Data
matchprobes Biocore Team c/o BioC user list Tools for sequence matching of probes on arrays
MergeMaid Xiaogang Zhong Merge Maid
metaArray Hyungwon Choi Integration of Microarray Data for Meta-analysis
Mfuzz Matthias Futschik Soft clustering of time series gene expression data
MiPP Sukwoo Kim Misclassification Penalized Posterior Classification
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
nem Florian Markowetz Nested Effects Models to reconstruct phenotypic hierarchies
nnNorm Adi Laurentiu Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
OCplus Alexander Ploner Operating characteristics plus sample size and local fdr for microarray experiments
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.
OrderedList Claudio Lottaz Similarities of Ordered Gene Lists
OutlierD Sukwoo Kim Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
pamr Rob Tibshirani Pam: prediction analysis for microarrays
pcot2 Sarah Song Principal Coordinates and Hotelling's T-Square method
PGSEA Karl Dykema Parametric Gene Set Enrichment Analysis
pickgene Brian S. Yandell Adaptive Gene Picking for Microarray Expression Data Analysis
plgem Mattia Pelizzola Power Law Global Error Model
puma Richard Pearson Propagating Uncertainty in Microarray Analysis
quantsmooth Jan Oosting Quantile smoothing and genomic visualization of array data
rama Raphael Gottardo Robust Analysis of MicroArrays
rbsurv Sukwoo Kim Robust likelihood-based survival modeling with microarray data
reb Karl J. Dykema Regional Expression Biases
RefPlus Kai-Ming Chang A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
Resourcerer Jianhua Zhang Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge.
rHVDM Martino Barenco Hidden Variable Dynamic Modeling
Ringo J. Toedling R Investigation of NimbleGen Oligoarrays
RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays
RMAGEML Steffen Durinck Handling MAGEML documents
RSNPper VJ Carey interface to for SNP-related data
safe William T. Barry Significance Analysis of Function and Expression
SAGx Per Broberg Statistical Analysis of the GeneChip
siggenes Holger Schwender Multiple testing using SAM and Efron's empirical Bayes approaches
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
sizepower Weiliang Qiu Sample Size and Power Calculation in Micorarray Studies
SMAP Robin Andersson A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
snapCGH John Marioni Segmentation, normalisation and processing of aCGH data.
SNPchip Robert Scharpf Classes and Methods for high throughput SNP chip data
spikeLI Enrico Carlon Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
splicegear Laurent splicegear
spotSegmentation Chris Fraley Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
ssize Gregory R. Warnes Estimate Microarry Sample Size
stepNorm Yuanyuan Xiao Stepwise normalization functions for cDNA microarrays
tilingArray W. Huber Analysis of high-density oligonucleotide tiling arrays
timecourse Yu Chuan Tai Statistical Analysis for Developmental Microarray Time Course Data
topGO Adrian Alexa topGO: Enrichment analysis for Gene Ontology
twilight Stefanie Scheid Estimation of local false discovery rate
VanillaICE Robert Scharpf Methods for fitting Hidden Markov Models to SNP chip data
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
webbioc Colin A. Smith Bioconductor Web Interface