| Package | Maintainer | Title |
|---|---|---|
| ACME | Sean Davis | Algorithms for Calculating Microarray Enrichment (ACME) |
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| BeadExplorer | Gareth Elvidge | QC, normalisation, annotation and exploration of Illumina BeadChip data |
| Biobase | Biocore Team | Biobase: Base functions for Bioconductor |
| bioDist | Biocore Team | Different distance measures |
| Category | S. Falcon | Category Analysis |
| CoCiteStats | R. Gentleman | Different test statistics based on co-citation. |
| CORREP | Dongxiao Zhu | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| 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 |
| EBarrays | Deepayan Sarkar | Empirical Bayes for Microarrays |
| edd | Vince Carey | expression density diagnostics |
| exonmap | Michal Okoniewski | High level analysis of Affymetrix exon array data |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| genefilter | Biocore Team | genefilter: methods for filtering genes from microarray experiments |
| GeneMeta | Biocore Team | MetaAnalysis for High Throughput Experiments |
| GGtools | Vince Carey | software and data for genetical genomics (c) 2006 VJ Carey |
| 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 |
| GOstats | S. Falcon | Tools for manipulating GO and microarrays. |
| gpls | Biocore Team | Classification using generalized partial least squares |
| GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| Icens | Biocore Team | NPMLE for Censored and Truncated Data |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
| 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 |
| LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| made4 | Aedin Culhane | Multivariate analysis of microarray data using ADE4 |
| MantelCorr | Brian Steinmeyer | Compute Mantel Cluster Correlations |
| MeasurementError.cor | Beiying Ding | Measurement Error model estimate for correlation coefficient |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| MLInterfaces | V. Carey | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
| nem | Florian Markowetz | Nested Effects Models to reconstruct phenotypic hierarchies |
| 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. |
| pcaMethods | Wolfram Stacklies | A collection of PCA methods. |
| puma | Richard Pearson | Propagating Uncertainty in Microarray Analysis |
| rbsurv | Sukwoo Kim | Robust likelihood-based survival modeling with microarray data |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| SAGx | Per Broberg | Statistical Analysis of the GeneChip |
| sigPathway | Weil Lai | Pathway Analysis |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| SLqPCR | Matthias Kohl | Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH |
| sscore | Richard Kennedy | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| ssize | Gregory R. Warnes | Estimate Microarry Sample Size |
| topGO | Adrian Alexa | topGO: Enrichment analysis for Gene Ontology |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |