| AnnotationDbi | Annotation Database Interface |
| base | The R Base Package |
| Biobase | Biobase: Base functions for Bioconductor |
| BiocGenerics | Generic functions for Bioconductor |
| BiocInstaller | Install/Update Bioconductor and CRAN Packages |
| boot | Bootstrap Functions (originally by Angelo Canty for S) |
| class | Functions for Classification |
| cluster | Cluster Analysis Extended Rousseeuw et al. |
| codetools | Code Analysis Tools for R |
| compiler | The R Compiler Package |
| corpcor | Efficient Estimation of Covariance and (Partial) Correlation |
| datasets | The R Datasets Package |
| DBI | R Database Interface |
| DynDoc | Dynamic document tools |
| e1071 | Misc Functions of the Department of Statistics (e1071), TU Wien |
| edgeR | Empirical analysis of digital gene expression data in R |
| fastICA | FastICA Algorithms to perform ICA and Projection Pursuit |
| fdrtool | Estimation of (Local) False Discovery Rates and Higher Criticism |
| foreign | Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ... |
| GeneCycle | Identification of Periodically Expressed Genes |
| graphics | The R Graphics Package |
| grDevices | The R Graphics Devices and Support for Colours and Fonts |
| grid | The Grid Graphics Package |
| Heatplus | Heatmaps with row and/or column covariates and colored clusters |
| IRanges | Infrastructure for manipulating intervals on sequences |
| KernSmooth | Functions for kernel smoothing for Wand & Jones (1995) |
| lattice | Lattice Graphics |
| limma | Linear Models for Microarray Data |
| longitudinal | Analysis of Multiple Time Course Data |
| maSigPro | Significant Gene Expression Profile Differences in Time Course
Microarray Data |
| MASS | Support Functions and Datasets for Venables and Ripley's MASS |
| Matrix | Sparse and Dense Matrix Classes and Methods |
| methods | Formal Methods and Classes |
| Mfuzz | Soft clustering of time series gene expression data |
| mgcv | Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
estimation |
| nlme | Linear and Nonlinear Mixed Effects Models |
| nnet | Feed-forward Neural Networks and Multinomial Log-Linear Models |
| parallel | Support for Parallel computation in R |
| rpart | Recursive Partitioning |
| RSQLite | SQLite interface for R |
| spatial | Functions for Kriging and Point Pattern Analysis |
| splines | Regression Spline Functions and Classes |
| stats | The R Stats Package |
| stats4 | Statistical Functions using S4 Classes |
| survival | Survival Analysis |
| tcltk | Tcl/Tk Interface |
| tkWidgets | R based tk widgets |
| tools | Tools for Package Development |
| utils | The R Utils Package |
| widgetTools | Creates an interactive tcltk widget |