| Package | Version | Title |
| aCGH | 1.1.7 | Classes and functions for Array Comparative Genomic Hybridization data. |
| affy | 1.6.7 | Methods for Affymetrix Oligonucleotide Arrays |
| affycomp | 1.4.3 | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| affydata | 1.4.1 | Affymetrix Data for Demonstration Purpose |
| affylmGUI | 1.2.7 | GUI for affy analysis using limma package |
| affypdnn | 1.1.0 | Probe Dependent Nearest Neighbours (PDNN) for the affy package |
| affyPLM | 1.3.3 | Methods for fitting probe-level models |
| altcdfenvs | 1.1.11 | alternative cdfenvs |
| annaffy | 1.0.18 | Annotation tools for Affymetrix biological metadata |
| AnnBuilder | 1.5.31 | Bioconductor annotation data package builder |
| annotate | 1.5.16 | Annotation for microarrays |
| apComplex | 1.1.5 | Estimate protein complex membership using AP-MS protein data |
| arrayMagic | 1.5.8 | two-colour cDNA array quality control and preprocessing |
| arrayQuality | 1.0.11 | Assessing array quality on spotted arrays |
| bim | 1.0.3 | Bayesian Interval Mapping Diagnostics |
| Biobase | 1.5.12 | Biobase: Base functions for Bioconductor |
| bioDist | 1.0.0 | Different distance measures |
| biomaRt | 1.0.4 | Interface to BioMart databases (e.g. Ensembl) |
| Biostrings | 1.1.1 | String objects reepresenting biological sequences |
| bridge | 1.0.1 | Bayesian Robust Inference for Differential Gene Expression |
| Category | 1.0.1 | Category Analysis |
| ChromoViz | 1.0 | Multimodal visualization of gene expression |
| CoCiteStats | 1.0.0 | Different test statistics based on co-citation. |
| convert | 1.1.11 | Convert Microarray Data Objects |
| ctc | 1.2.7 | Cluster and Tree Conversion. |
| daMA | 1.0.1 | Efficient design and analysis of factorial two-colour microarray data |
| DEDS | 1.0.5 | Differential Expression via Distance Summary for Microarray Data |
| DNAcopy | 1.1.2 | DNA copy number data analysis |
| DynDoc | 1.5.5 | Dynamic document tools |
| EBarrays | 1.0.19 | Empirical Bayes for Microarrays |
| ecolitk | 1.0.1 | Meta-data and tools for E. coli |
| edd | 1.5.1 | expression density diagnostics |
| factDesign | 1.1.5 | Factorial designed microarray experiment analysis |
| gcrma | 1.1.4 | Background Adjustment Using Sequence Information |
| genArise | 1.3.2 | Microarray Analysis tool |
| genefilter | 1.6.3 | genefilter: filter genes |
| GeneMeta | 1.0.0 | MetaAnalysis for High Throughput Experiments |
| geneplotter | 1.6.1 | Grapics related functions for Bioconductor |
| geneRecommender | 1.0.2 | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneSpring | 2.0.0 | GeneSpring R Integration Functions |
| GeneTraffic | 1.0.6 | GeneTraffic R Integration Functions |
| GeneTS | 2.4.1 | Microarray Time Series and Network Analysis |
| gff3Plotter | 1.0.2 | Structuring and Plotting GFF3 Data Files |
| GLAD | 1.0.4 | Gain and Loss Analysis of DNA |
| globaltest | 3.0.5 | Testing Association of a Group of Genes with a Clinical Variable |
| goCluster | 1.0.3 | Analysis of clustering results in conjunction with annotation data. |
| GOstats | 1.1.3 | Tools for manipulating GO and microarrays. |
| goTools | 1.0.6 | Functions for Gene Ontology database |
| gpls | 1.0.6 | Classification using generalized partial least squares |
| graph | 1.5.9 | graph: A package to handle graph data structures |
| GraphAT | 1.0.0 | Graph Theoretic Association Tests |
| hexbin | 1.2.7 | Hexagonal Binning Routines |
| hopach | 1.1.1 | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| hypergraph | 1.0.0 | A package providing hypergraph data structures |
| Icens | 1.0.0 | NPMLE for Censored and Truncated Data |
| ideogram | 1.0.1 | ideogram |
| impute | 1.0.2 | impute: Imputation for microarray data |
| iSPlot | 1.0.8 | Linking Plots |
| KEGGSOAP | 1.1.5 | Client-side SOAP access KEGG |
| limma | 1.9.6 | Linear Models for Microarray Data |
| limmaGUI | 1.3.9 | GUI for limma package |
| LPE | 1.1.5 | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| macat | 1.2.0 | MicroArray Chromosome Analysis Tool |
| maDB | 1.0.1 | Micro array database and utility functions for micro array analysis. |
| made4 | 1.0.0 | Multivariate analysis of microarray data using ADE4 |
| makecdfenv | 1.5.2 | CDF Environment Maker |
| marray | 1.6.3 | Exploratory analysis for two-color spotted microarray data |
| matchprobes | 1.0.22 | Tools for sequence matching of probes on arrays |
| MCRestimate | 1.2.6 | Misclassification error estimation with cross-validation |
| MeasurementError.cor | 1.0.2 | Measurement Error model estimate for correlation coefficient |
| MergeMaid | 2.0.1 | Merge Maid |
| MiPP | 1.0.2 | MiPP (Misclassification Penalized Posterior)-based Classification |
| MLInterfaces | 1.0.10 | MLInterfaces |
| msbase | 1.1.1 | Basic classes and methods for mass spectrometric mass list manipulation. |
| mscalib | 1.0.2 | Calibration and filtering of mass spectrometric peak(mass) lists. |
| multtest | 1.6.0 | Resampling-based multiple hypothesis testing |
| nnNorm | 1.1.0 | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| OLIN | 1.3.3 | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | 1.0.1 | Graphical user interface for OLIN |
| ontoTools | 1.4.8 | graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management |
| pairseqsim | 1.0.4 | pairwise sequence alignment similarity simple. |
| pamr | 1.22 | Pam: prediction analysis for microarrays |
| pgUtils | 1.0.3 | Utility functions for PostgreSQL databases |
| pickgene | 1.0.0 | Adaptive Gene Picking for Microarray Expression Data Analysis |
| plgem | 1.0.0 | Power Law Global Error Model |
| plier | 1.0.0 | Implements the Affymetrix PLIER algorithm |
| prada | 1.3.1 | Data analysis for cell-based functional assays |
| PROcess | 1.3.4 | Ciphergen SELDI-TOF Processing |
| qvalue | 1.1.0 | Q-value estimation for false discovery rate control |
| rama | 1.0.1 | Robust Analysis of MicroArrays |
| RankProd | 1.0.0 | Rank Product method for identifying differentially expressed genes. |
| RBGL | 1.3.13 | Test interface to boost C++ graph lib |
| Rdbi | 1.1.2 | Generic database methods |
| RdbiPgSQL | 1.1.4 | PostgreSQL access |
| reposTools | 1.5.19 | Repository tools for R |
| Resourcerer | 1.1.2 | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| rfcdmin | 1.0.0 | Minimal Data Library for RFlowCyt examples |
| rflowcyt | 1.0.1 | Statistical tools and data structures for analytic flow cytometry |
| Rgraphviz | 1.5.10 | Provides plotting capabilities for R graph objects |
| rhdf5 | 1.4.1 | An HDF5 interface for R |
| ROC | 1.1.1 | utilities for ROC, with uarray focus |
| RSNPper | 1.0.5 | interface to chip.org::SNPper for SNP-related data |
| Ruuid | 1.5.3 | Ruuid: Provides Universally Unique ID values |
| safe | 1.0.0 | Significance Analysis of Function and Expression |
| SAGElyzer | 1.5.2 | A package that deals with SAGE libraries |
| sagenhaft | 1.0.0 | Collection of functions for reading and comparing SAGE libraries |
| siggenes | 1.2.17 | SAM and Efron's empirical Bayes approaches |
| simpleaffy | 2.0.16 | Very simple high level analysis of Affymetrix data |
| SNAData | 1.1.1 | Social Networks Analysis Data Examples |
| splicegear | 1.0.10 | splicegear |
| spotSegmentation | 1.1.1 | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| ssize | 1.0.1 | Estimate Microarry Sample Size |
| stam | 1.0.9 | Structured Analysis of Microarray Data |
| stepNorm | 1.0.2 | Stepwise normalization functions for cDNA microarrays |
| tilingArray | 1.0.2 | Analysis of tiling arrays |
| tkWidgets | 1.5.23 | R based tk widgets |
| twilight | 1.1.0 | Estimation of local false discovery rate |
| vsn | 1.6.3 | Variance stabilization and calibration for microarray data |
| webbioc | 1.0.1 | Bioconductor Web Interface |
| widgetInvoke | 1.0.0 | Evaluation widgets for functions |
| widgetTools | 1.4.7 | Creates an interactive tcltk widget |
| xcms | 1.0.0 | LC/MS and GC/MS Data Analysis |