| Package | Maintainer | Title |
|---|---|---|
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| BCRANK | Adam Ameur | Predicting binding site consensus from ranked DNA sequences |
| betr | Martin Aryee | Identify differentially expressed genes in microarray time-course data |
| bgafun | Iain Wallace | BGAfun A method to identify specifity determining residues in protein families |
| BGmix | Alex Lewin | Bayesian models for differential gene expression |
| BicARE | Pierre Gestraud | Biclustering Analysis and Results Exploration |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| ChemmineR | Y. Eddie Cao | A Compound Data Mining Framework |
| clusterStab | James W. MacDonald | Compute cluster stability scores for microarray data |
| CMA | Martin Slawski | Synthesis of microarray-based classification |
| CORREP | Dongxiao Zhu | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| cosmo | Oliver Bembom | Supervised detection of conserved motifs in DNA sequences |
| cosmoGUI | Oliver Bembom | GUI for constructing constraint sets used by the cosmo package |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| flowClust | Raphael Gottardo | Clustering for Flow Cytometry |
| gaga | David Rossell | GaGa hierarchical model for microarray data analysis |
| gene2pathway | Holger Froehlich | Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures |
| geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| GOSemSim | Guangchuang Yu | GO-terms Semantic Similarity Measures |
| GOstats | Robert Gentleman | Tools for manipulating GO and microarrays. |
| gpls | Biocore Team c/o BioC user list | Classification using generalized partial least squares |
| hopach | Katherine S. Pollard | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| iterativeBMA | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) algorithm |
| LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| logicFS | Holger Schwender | Identification of SNP Interactions |
| maanova | Keith Sheppard | Tools for analyzing Micro Array experiments |
| made4 | Aedin Culhane | Multivariate analysis of microarray data using ADE4 |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| MantelCorr | Brian Steinmeyer | Compute Mantel Cluster Correlations |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differences in Time Course Microarray Data |
| MCRestimate | Marc Johannes | Misclassification error estimation with cross-validation |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| microRNA | Robert Gentleman | Data and functions for dealing with microRNAs |
| MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
| MLInterfaces | V. Carey | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| 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 |
| pamr | Rob Tibshirani | Pam: prediction analysis for microarrays |
| parody | VJ Carey | Parametric And Resistant Outlier DYtection |
| pdmclass | James W. MacDonald | Classification of Microarray Samples using Penalized Discriminant Methods |
| puma | Richard Pearson | Propagating Uncertainty in Microarray Analysis |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| Rmagpie | Camille Maumet | MicroArray Gene-expression-based Program In Error rate estimation |
| rMAT | Arnaud Droit and Raphael Gottardo | R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| seqLogo | Oliver Bembom | Sequence logos for DNA sequence alignments |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| sigPathway | Weil Lai | Pathway Analysis |
| SSPA | Maarten van Iterson | Sample Size and Power Analysis for Microarray Data |
| stam | Claudio Lottaz | Structured Analysis of Microarray Data |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| vbmp | Nicola Lama | Variational Bayesian Multinomial Probit Regression |