Package Index


[Top]

Packages in the standard library

ALLA data package
AnnBuilderBioconductor annotation data package builder
BiobaseBiobase: Base functions for Bioconductor
BiostringsString objects reepresenting biological sequences
ChromoVizMultimodal visualization of gene expression
DEDSDifferential Expression via Distance Summary for Microarray Data
DNAcopyDNA copy number data analysis
DynDocDynamic document tools
EBarraysEmpirical Bayes for Microarrays
GLADGain and Loss Analysis of DNA
GOA data package containing annotation data for GO
GOstatsTools for manipulating GO and microarrays.
GeneSpringGeneSpring R Integration Functions
GeneTSGenetic Time Series and Graphical Models
GraphATGraph Theoretic Association Tests
HEMHeterogeneous error model for analysis of microarray data
IcensNPMLE for Censored and Truncated Data
KEGGA data package containing annotation data for KEGG
KEGGSOAPClient-side SOAP access KEGG
KernSmoothFunctions for kernel smoothing for Wand & Jones (1995)
LPEMethods for analyzing microarray data using Local Pooled Error (LPE) method
MASSMain Package of Venables and Ripley's MASS
MCMCpackMarkov chain Monte Carlo (MCMC) Package
MLInterfacesMLInterfaces
MeasurementError.corMeasurement Error model estimate for correlation coefficient
MergeMaidMerge Maid
OLINOptimized local intensity-dependent normalisation of two-color microarrays
OLINguiGraphical user interface for OLIN
PROcessCiphergen SELDI-TOF Processing
R2HTMLHTML exportation for R objects
RColorBrewerColorBrewer palettes
RGtkInitial R bindings for Gtk
RMAGEMLHandling MAGEML documents
ROCutilities for ROC, with uarray focus
RSNPperinterface to chip.org::SNPper for SNP-related data
RSvgDeviceAn R SVG graphics device.
RdbiGeneric database methods
ResourcererReads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge.
RuuidRuuid: Provides Universally Unique ID values
SAGElyzerA package that deals with SAGE libraries
SNADataSocial Networks Analysis Data Examples
SparseMSparse Linear Algebra
XMLTools for parsing and generating XML within R and S-Plus.
YEASTA data package containing annotation data for YEAST
aCGHClasses and functions for Array Comparative Genomic Hybridization data.
affyMethods for Affymetrix Oligonucleotide Arrays
affyPLMMethods for fitting probe-level models
affycompGraphics Toolbox for Assessment of Affymetrix Expression Measures
affydataAffymetrix Data for Demonstration Purpose
affylmGUIGUI for affy analysis using limma package
affypdnnProbe Dependent Nearest Neighbours (PDNN) for the affy package
altcdfenvsalternative cdfenvs
annaffyAnnotation tools for Affymetrix biological metadata
annotateAnnotation for microarrays
arrayMagictwo-colour cDNA array quality control and preprocessing
arrayQualityAssessing array quality on spotted arrays
awsAdaptive Weights Smoothing
baseThe R Base Package
bimBayesian Interval Mapping Diagnostics
bootBootstrap R (S-Plus) Functions (Canty)
classFunctions for Classification
clusterCluster Analysis Extended Rousseeuw et al.
codaOutput analysis and diagnostics for MCMC
convertConvert Microarray Data Objects
ctcCluster and Tree Conversion.
ctestClassical Tests
daMAEfficient design and analysis of factorial two-colour microarray data
datasetsThe R Datasets Package
e1071Misc Functions of the Department of Statistics (e1071), TU Wien
ecolitkMeta-data and tools for E. coli
edaExploratory Data Analysis
eddexpression density diagnostics
exprExternalImplementation of exprSet using externalVectors
externalVectorVector objects for R with external storage
factDesignFactorial designed microarray experiment analysis
fdaFunctional Data Analysis
fibroEsetexprSet for Karaman et al. (2003) fibroblasts data
foreignRead Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ...
gbmGeneralized Boosted Regression Models
gcrmaBackground Adjustment Using Sequence Information
genAriseMicroarray Analysis tool
genefiltergenefilter: filter genes
geneplotterGrapics related functions for Bioconductor
globaltestTesting Association of a Group of Genes with a Clinical Variable
goClusterAnalysis of clustering results in conjunction with annotation data.
goToolsFunctions for Gene Ontology database
golubEsetsexprSets for golub leukemia data
gplsClassification using generalized partial least squares
grDevicesThe R Graphics Devices and Support for Colours and Fonts
graphicsThe R Graphics Package
gridThe Grid Graphics Package
gtkDeviceLoadable gtk device driver for R
gtkWidgetsWidgets built using RGtk
hexbinHexagonal Binning Routines ___OLD VERSION___
hgu133aA data package containing annotation data for hgu133a
hgu133acdfhgu133acdf
hgu95acdfhgu95acdf
hgu95av2Affymetrix Human Genome U95 Set Annotation Data (hgu95av2)
hgu95av2cdfhgu95av2cdf
hgu95av2probeProbe sequence data for microarrays of type hgu95av2
hopachHierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
hsahomologyA data package containing annotation data for hsahomology
hu6800A data package containing annotation data for hu6800
hu6800cdfhu6800cdf
hu6800probeProbe sequence data for microarrays of type hugenefl
iSPlotLinking Plots
imputeimpute: Imputation for microarray data
ipredImproved Predictors
latticeLattice Graphics
limmaLinear Models for Microarray Data
locfitLocal Regression, Likelihood and Density Estimation.
lqsResistant Regression and Covariance Estimation
makecdfenvCDF Environment Maker
marrayExploratory analysis for two-color spotted microarray data
matchprobesTools for sequence matching of probes on arrays
methodsFormal Methods and Classes
mgcvGAMs with GCV smoothness estimation and GAMMs by REML/PQL
mlbenchMachine Learning Benchmark Problems
mleMaximum likelihood estimation
modregModern Regression: Smoothing and Local Methods
msbaseBasic classes and methods for mass spectrometric mass list manipulation.
multtestResampling-based multiple hypothesis testing
mvaClassical Multivariate Analysis
mvtnormMultivariate Normal and T Distribution
nlmeLinear and nonlinear mixed effects models
nlsNonlinear Regression
nnNormSpatial and intensity based normalization of cDNA microarray data based on robust neural nets
nnetFeed-forward Neural Networks and Multinomial Log-Linear Models
pairseqsimpairwise sequence alignment similarity simple.
pamrPam: prediction analysis for microarrays
pickgeneAdaptive Gene Picking for Microarray Expression Data Analysis
plasmodiumanophelescdfplasmodiumanophelescdf
pradaData analysis for cell-based assays
qtlTools for analyzing QTL experiments
qvalueQ-value estimation for false discovery rate control
rae230aA data package containing annotation data for rae230a
rae230aprobeProbe sequence data for microarrays of type rae230a
ramaRobust Analysis of MicroArrays
randomForestBreiman and Cutler's random forests for classification and regression
repeatedNon-normal Repeated Measurements Models
reposToolsRepository tools for R
rmutilUtilities for Nonlinear Regression and Repeated Measurements Models
rpartRecursive Partitioning
rrcovScalable Robust Estimators with High Breakdown Point
siggenesSAM and Efron's empirical Bayes approaches
simpleaffyVery simple high level analysis of Affymetrix data
smaStatistical Microarray Analysis
snowSimple Network of Workstations
spatialFunctions for Kriging and Point Pattern Analysis
splinesRegression Spline Functions and Classes
stamStructured Analysis of Microarray Data
statmodStatistical Modeling
statsThe R Stats Package
stats4Statistical Functions using S4 Classes
stepNormStepwise normalization functions for cDNA microarrays
stepfunStep Functions, including Empirical Distributions
survivalSurvival analysis, including penalised likelihood.
tcltkTcl/Tk Interface
tkWidgetsR based tk widgets
tkrplotTK Rplot
toolsTools for Package Development
tsTime Series Functions
utilsThe R Utils Package
vsnVariance stabilization and calibration for microarray data
webbiocBioconductor Web Interface
widgetInvokeEvaluation widgets for functions
widgetToolsCreates an interactive tcltk widget
xenopuslaevisA data package containing annotation data for xenopuslaevis
xlahomologyA data package containing annotation data for xlahomology
xtableExport tables to LaTeX or HTML
zebrafishA data package containing annotation data for zebrafish