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.
adSplit Claudio Lottaz Annotation-Driven Clustering
affy Rafael A. Irizarry Methods for Affymetrix Oligonucleotide Arrays
affycomp Rafael A. Irizarry Graphics Toolbox for Assessment of Affymetrix Expression Measures
AffyCompatible Martin Morgan Affymetrix GeneChip software compatibility
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
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
affyQCReport Craig Parman QC Report Generation for affyBatch objects
Agi4x44PreProcess Pedro Lopez-Romero PreProcessing of Agilent 4x44 array data
altcdfenvs Laurent Gautier alternative CDF environments (aka mappings)
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
ArrayExpress Audrey Kauffmann Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
arrayMvout V. Carey multivariate outlier detection for expression array QA
arrayQuality Agnes Paquet Assessing array quality on spotted arrays
arrayQualityMetrics Audrey Kauffmann Quality metrics on microarray data sets
ArrayTools Arthur Li geneChip Analysis Package
BAC Raphael Gottardo Bayesian Analysis of Chip-chip experiment
beadarray Mark Dunning Quality assessment and low-level analysis for Illumina BeadArray data
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
BGmix Alex Lewin Bayesian models for differential gene expression
bgx Ernest Turro Bayesian Gene eXpression
BicARE Pierre Gestraud , BicARE
bridge Raphael Gottardo Bayesian Robust Inference for Differential Gene Expression
CALIB Hui Zhao Calibration model for estimating absolute expression levels from microarray data
CGHbase Sjoerd Vosse CGHbase: Base functions and classes for arrayCGH data analysis.
CGHcall Sjoerd Vosse Calling aberrations for array CGH tumor profiles.
cghMCR J. Zhang Find chromosome regions showing common gains/losses
CGHregions Sjoerd Vosse Dimension Reduction for Array CGH Data with Minimal Information Loss.
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
DFP Rodrigo Alvarez-Glez Gene Selection
diffGeneAnalysis Choudary Jagarlamudi Performs differential gene expression Analysis
DNAcopy Venkatraman E. Seshan DNA copy number data analysis
dualKS Eric J. Kort Dual KS Discriminant Analysis and Classification
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
GenomeGraphs Steffen Durinck Plotting genomic information from Ensembl
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
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
goProfiles Alex Sanchez goProfiles: an R package for the statistical analysis of functional profiles
goTools Agnes Paquet Functions for Gene Ontology database
gpls Biocore Team c/o BioC user list Classification using generalized partial least squares
GSEAlm Assaf Oron Linear Model Toolset for Gene Set Enrichment Analysis
Heatplus Alexander Ploner A heat map displaying covariates and coloring clusters
HELP Reid F. Thompson Tools for HELP data analysis
HEM HyungJun Cho Heterogeneous error model for identification of differentially expressed genes under multiple conditions
impute Balasubramanian Narasimhan impute: Imputation for microarray data
ITALICS Guillem Rigaill ITALICS
iterativeBMA Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) algorithm
iterativeBMAsurv Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
KCsmart Jorma de Ronde Multi sample aCGH analysis package using kernel convolution
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
logitT Tobias Guennel logit-t Package
LPE Nitin Jain Methods for analyzing microarray data using Local Pooled Error (LPE) method
LPEadj Carl Murie A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
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 Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment
MEDME Mattia Pelizzola Modelling Experimental Data from MeDIP Enrichment
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
minet Patrick E. Meyer Mutual Information Network Inference
MiPP Sukwoo Kim Misclassification Penalized Posterior Classification
multiscan Mizanur Khondoker R package for combining multiple scans
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
nudge N. Dean Normal Uniform Differential Gene Expression detection
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. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files.
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
PLPE Soo-heang Eo Local Pooled Error Test for Differential Expression with Paired High-throughput Data
plw Magnus Astrand Probe level Locally moderated Weighted t-tests.
puma Richard Pearson Propagating Uncertainty in Microarray Analysis
rama Raphael Gottardo Robust Analysis of MicroArrays
rbsurv Sooheang Eo 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 ChIP-chip Oligoarrays
RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays
RMAGEML Steffen Durinck Handling MAGEML documents
SAGx Per Broberg, Statistical Analysis of the GeneChip
siggenes Holger Schwender Multiple testing using SAM and Efron's empirical Bayes approaches
SIM Maarten van Iterson Integrated Analysis of gene expression and copynumber data
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 Thomas Hardcastle Segmentation, normalisation and processing of aCGH data.
snpMatrix David Clayton The snp.matrix and X.snp.matrix classes
spikeLI Enrico Carlon Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
spotSegmentation Chris Fraley Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
ssize Gregory R. Warnes Estimate Microarray Sample Size
stam Claudio Lottaz Structured Analysis of Microarray Data
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
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
webbioc Colin A. Smith Bioconductor Web Interface
XDE Robert Scharpf XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
xps Christian Stratowa Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
yaqcaffy Laurent Gatto Affymetrix expression data quality control and reproducibility analysis