Bioconductor Task View: AssayDomains

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Package Maintainer Title
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
affylmGUI Keith Satterley GUI for affy analysis using limma package
altcdfenvs Laurent Gautier alternative CDF environments (aka mappings)
ArrayTools Arthur Li geneChip Analysis Package
BAC Raphael Gottardo Bayesian Analysis of Chip-chip experiment
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
cellHTS Ligia Bras Analysis of cell-based screens
cellHTS2 Florian Hahne Analysis of cell-based screens - revised version of cellHTS
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
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
edd Vince Carey expression density diagnostics
edgeR Mark Robinson Empirical analysis of digital gene expression data in R
exonmap Crispin Miller High level analysis of Affymetrix exon array data
factDesign Denise Scholtens Factorial designed microarray experiment analysis
fdrame Effi Kenigsberg FDR adjustments of Microarray Experiments (FDR-AME)
flowCore Nolwenn Le Meur flowCore: Basic structures for flow cytometry data
flowQ N. Le Meur Qualitiy control for flow cytometry
flowUtils Nishant Gopalakrishnan Utilities for flow cytometry
flowViz Florian Hahne Visualization for flow cytometry
gaga David Rossell GaGa hierarchical model for microarray data analysis
GeneSelector Martin Slawski GeneSelector
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
HEM HyungJun Cho Heterogeneous error model for identification of differentially expressed genes under multiple conditions
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
maanova Hyuna Yang Tools for analyzing Micro Array experiments
macat Joern Toedling MicroArray Chromosome Analysis Tool
maigesPack Gustavo H. Esteves Functions to handle cDNA microarray data, including several methods of data analysis
maSigPro Ana Conesa Significant Gene Expression Profile Differeneces in Time Course Microarray Data
MEDME Mattia Pelizzola Modelling Experimental Data from MeDIP Enrichment
MergeMaid Xiaogang Zhong Merge Maid
metaArray Hyungwon Choi Integration of Microarray Data for Meta-analysis
miRNApath James M. Ward miRNApath: Pathway Enrichment for miRNA Expression Data
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
nudge N. Dean Normal Uniform Differential Gene Expression detection
OCplus Alexander Ploner Operating characteristics plus sample size and local fdr for microarray experiments
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
pcot2 Sarah Song Principal Coordinates and Hotelling's T-Square method
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.
prada Florian Hahne Data analysis for cell-based functional assays
puma Richard Pearson Propagating Uncertainty in Microarray Analysis
RankProd Fangxin Hong Rank Product method for identifying differentially expressed genes with application in meta-analysis
rflowcyt N. LeMeur Statistical tools and data structures for analytic flow cytometry
rHVDM Martino Barenco Hidden Variable Dynamic Modeling
RNAither Nora Rieber Statistical analysis of high-throughput RNAi screens
ROC Vince Carey utilities for ROC, with uarray focus
SAGx Per Broberg, Statistical Analysis of the GeneChip
siggenes Holger Schwender Multiple testing using SAM and Efron's empirical Bayes approaches
sigPathway Weil Lai Pathway Analysis
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
splicegear Laurent Gautier splicegear
sscore Richard Kennedy S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
ssize Gregory R. Warnes Estimate Microarray Sample Size
timecourse Yu Chuan Tai Statistical Analysis for Developmental Microarray Time Course Data
twilight Stefanie Scheid Estimation of local false discovery rate
webbioc Colin A. Smith Bioconductor Web Interface
XDE Robert Scharpf XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression