ALL | A data package |

AnnBuilder | Bioconductor annotation data package builder |

Biobase | Biobase: Base functions for Bioconductor |

Biostrings | String objects reepresenting biological sequences |

ChromoViz | Multimodal visualization of gene expression |

DEDS | Differential Expression via Distance Summary for Microarray Data |

DNAcopy | DNA copy number data analysis |

DynDoc | Dynamic document tools |

EBarrays | Empirical Bayes for Microarrays |

GLAD | Gain and Loss Analysis of DNA |

GO | A data package containing annotation data for GO |

GOstats | Tools for manipulating GO and microarrays. |

GeneSpring | GeneSpring R Integration Functions |

GeneTS | Genetic Time Series and Graphical Models |

GraphAT | Graph Theoretic Association Tests |

HEM | Heterogeneous error model for analysis of microarray data |

Icens | NPMLE for Censored and Truncated Data |

KEGG | A data package containing annotation data for KEGG |

KEGGSOAP | Client-side SOAP access KEGG |

KernSmooth | Functions for kernel smoothing for Wand & Jones (1995) |

LPE | Methods for analyzing microarray data using Local Pooled Error (LPE) method |

MASS | Main Package of Venables and Ripley's MASS |

MCMCpack | Markov chain Monte Carlo (MCMC) Package |

MLInterfaces | MLInterfaces |

MeasurementError.cor | Measurement Error model estimate for correlation coefficient |

MergeMaid | Merge Maid |

OLIN | Optimized local intensity-dependent normalisation of two-color microarrays |

OLINgui | Graphical user interface for OLIN |

PROcess | Ciphergen SELDI-TOF Processing |

R2HTML | HTML exportation for R objects |

RColorBrewer | ColorBrewer palettes |

RGtk | Initial R bindings for Gtk |

RMAGEML | Handling MAGEML documents |

ROC | utilities for ROC, with uarray focus |

RSNPper | interface to chip.org::SNPper for SNP-related data |

RSvgDevice | An R SVG graphics device. |

Rdbi | Generic database methods |

Resourcerer | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |

Ruuid | Ruuid: Provides Universally Unique ID values |

SAGElyzer | A package that deals with SAGE libraries |

SNAData | Social Networks Analysis Data Examples |

SparseM | Sparse Linear Algebra |

XML | Tools for parsing and generating XML within R and S-Plus. |

YEAST | A data package containing annotation data for YEAST |

aCGH | Classes and functions for Array Comparative Genomic Hybridization data. |

affy | Methods for Affymetrix Oligonucleotide Arrays |

affyPLM | Methods for fitting probe-level models |

affycomp | Graphics Toolbox for Assessment of Affymetrix Expression Measures |

affydata | Affymetrix Data for Demonstration Purpose |

affylmGUI | GUI for affy analysis using limma package |

affypdnn | Probe Dependent Nearest Neighbours (PDNN) for the affy package |

altcdfenvs | alternative cdfenvs |

annaffy | Annotation tools for Affymetrix biological metadata |

annotate | Annotation for microarrays |

arrayMagic | two-colour cDNA array quality control and preprocessing |

arrayQuality | Assessing array quality on spotted arrays |

aws | Adaptive Weights Smoothing |

base | The R Base Package |

bim | Bayesian Interval Mapping Diagnostics |

boot | Bootstrap R (S-Plus) Functions (Canty) |

class | Functions for Classification |

cluster | Cluster Analysis Extended Rousseeuw et al. |

coda | Output analysis and diagnostics for MCMC |

convert | Convert Microarray Data Objects |

ctc | Cluster and Tree Conversion. |

ctest | Classical Tests |

daMA | Efficient design and analysis of factorial two-colour microarray data |

datasets | The R Datasets Package |

e1071 | Misc Functions of the Department of Statistics (e1071), TU Wien |

ecolitk | Meta-data and tools for E. coli |

eda | Exploratory Data Analysis |

edd | expression density diagnostics |

exprExternal | Implementation of exprSet using externalVectors |

externalVector | Vector objects for R with external storage |

factDesign | Factorial designed microarray experiment analysis |

fda | Functional Data Analysis |

fibroEset | exprSet for Karaman et al. (2003) fibroblasts data |

foreign | Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... |

gbm | Generalized Boosted Regression Models |

gcrma | Background Adjustment Using Sequence Information |

genArise | Microarray Analysis tool |

genefilter | genefilter: filter genes |

geneplotter | Grapics related functions for Bioconductor |

globaltest | Testing Association of a Group of Genes with a Clinical Variable |

goCluster | Analysis of clustering results in conjunction with annotation data. |

goTools | Functions for Gene Ontology database |

golubEsets | exprSets for golub leukemia data |

gpls | Classification using generalized partial least squares |

grDevices | The R Graphics Devices and Support for Colours and Fonts |

graphics | The R Graphics Package |

grid | The Grid Graphics Package |

gtkDevice | Loadable gtk device driver for R |

gtkWidgets | Widgets built using RGtk |

hexbin | Hexagonal Binning Routines ___OLD VERSION___ |

hgu133a | A data package containing annotation data for hgu133a |

hgu133acdf | hgu133acdf |

hgu95acdf | hgu95acdf |

hgu95av2 | Affymetrix Human Genome U95 Set Annotation Data (hgu95av2) |

hgu95av2cdf | hgu95av2cdf |

hgu95av2probe | Probe sequence data for microarrays of type hgu95av2 |

hopach | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |

hsahomology | A data package containing annotation data for hsahomology |

hu6800 | A data package containing annotation data for hu6800 |

hu6800cdf | hu6800cdf |

hu6800probe | Probe sequence data for microarrays of type hugenefl |

iSPlot | Linking Plots |

impute | impute: Imputation for microarray data |

ipred | Improved Predictors |

lattice | Lattice Graphics |

limma | Linear Models for Microarray Data |

locfit | Local Regression, Likelihood and Density Estimation. |

lqs | Resistant Regression and Covariance Estimation |

makecdfenv | CDF Environment Maker |

marray | Exploratory analysis for two-color spotted microarray data |

matchprobes | Tools for sequence matching of probes on arrays |

methods | Formal Methods and Classes |

mgcv | GAMs with GCV smoothness estimation and GAMMs by REML/PQL |

mlbench | Machine Learning Benchmark Problems |

mle | Maximum likelihood estimation |

modreg | Modern Regression: Smoothing and Local Methods |

msbase | Basic classes and methods for mass spectrometric mass list manipulation. |

multtest | Resampling-based multiple hypothesis testing |

mva | Classical Multivariate Analysis |

mvtnorm | Multivariate Normal and T Distribution |

nlme | Linear and nonlinear mixed effects models |

nls | Nonlinear Regression |

nnNorm | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |

nnet | Feed-forward Neural Networks and Multinomial Log-Linear Models |

pairseqsim | pairwise sequence alignment similarity simple. |

pamr | Pam: prediction analysis for microarrays |

pickgene | Adaptive Gene Picking for Microarray Expression Data Analysis |

plasmodiumanophelescdf | plasmodiumanophelescdf |

prada | Data analysis for cell-based assays |

qtl | Tools for analyzing QTL experiments |

qvalue | Q-value estimation for false discovery rate control |

rae230a | A data package containing annotation data for rae230a |

rae230aprobe | Probe sequence data for microarrays of type rae230a |

rama | Robust Analysis of MicroArrays |

randomForest | Breiman and Cutler's random forests for classification and regression |

repeated | Non-normal Repeated Measurements Models |

reposTools | Repository tools for R |

rmutil | Utilities for Nonlinear Regression and Repeated Measurements Models |

rpart | Recursive Partitioning |

rrcov | Scalable Robust Estimators with High Breakdown Point |

siggenes | SAM and Efron's empirical Bayes approaches |

simpleaffy | Very simple high level analysis of Affymetrix data |

sma | Statistical Microarray Analysis |

snow | Simple Network of Workstations |

spatial | Functions for Kriging and Point Pattern Analysis |

splines | Regression Spline Functions and Classes |

stam | Structured Analysis of Microarray Data |

statmod | Statistical Modeling |

stats | The R Stats Package |

stats4 | Statistical Functions using S4 Classes |

stepNorm | Stepwise normalization functions for cDNA microarrays |

stepfun | Step Functions, including Empirical Distributions |

survival | Survival analysis, including penalised likelihood. |

tcltk | Tcl/Tk Interface |

tkWidgets | R based tk widgets |

tkrplot | TK Rplot |

tools | Tools for Package Development |

ts | Time Series Functions |

utils | The R Utils Package |

vsn | Variance stabilization and calibration for microarray data |

webbioc | Bioconductor Web Interface |

widgetInvoke | Evaluation widgets for functions |

widgetTools | Creates an interactive tcltk widget |

xenopuslaevis | A data package containing annotation data for xenopuslaevis |

xlahomology | A data package containing annotation data for xlahomology |

xtable | Export tables to LaTeX or HTML |

zebrafish | A data package containing annotation data for zebrafish |