Hallo,
I just installed all needed packages for my project on my PC. But I cannot load
all at one time. I now want to load limma. How can I realize the following
plan: I want to install for example limma inclusive all needed other sub
packages (add-on). Can anyone tell me the corresponding command?
Thanks, Corinna
Here is the result of the command library():
Pakete in Library 'D:/R/R-2.6.0/library':
ada Performs boosting algorithms for a binary
response
affy Methods for Affymetrix Oligonucleotide Arrays
affycomp Graphics Toolbox for Assessment of Affymetrix
Expression Measures
affydata Affymetrix Data for Demonstration Purpose
affyio Tools for parsing Affymetrix data files
affyPLM Methods for fitting probe-level models
affyQCReport QC Report Generation for affyBatch objects
ALL A data package
annaffy Annotation tools for Affymetrix biological
metadata
annotate Annotation for microarrays
AnnotationDbi Annotation Database Interface
arules Mining Association Rules and Frequent Itemsets
base The R Base Package
Biobase Biobase: Base functions for Bioconductor
biomaRt Interface to BioMart databases (e.g. Ensembl,
Wormbase, Gramene and Uniprot)
Biostrings String objects representing biological
sequences, and matching algorithms
boot Bootstrap R (S-Plus) Functions (Canty)
Category Category Analysis
CCl4 Carbon Tetrachloride (CCl4) treated hepatocytes
class Functions for Classification
cluster Cluster Analysis Extended Rousseeuw et al.
codetools Code Analysis Tools for R
datasets The R Datasets Package
DBI R Database Interface
DynDoc Dynamic document tools
e1071 Misc Functions of the Department of Statistics
(e1071), TU Wien
edd expression density diagnostics
foreign Read Data Stored by Minitab, S, SAS, SPSS,
Stata, Systat, dBase, ...
gcrma Background Adjustment Using Sequence
Information
genefilter genefilter: methods for filtering genes from
microarray experiments
geneplotter Grapics related functions for Bioconductor
globaltest Testing Association of Groups of Genes with a
Clinical Variable
GO A data package containing annotation data for
GO
GO.db A set of annotation maps describing the entire
Gene Ontology
golubEsets exprSets for golub leukemia data
GOstats Tools for manipulating GO and microarrays.
graph graph: A package to handle graph data
structures
graphics The R Graphics Package
grDevices The R Graphics Devices and Support for Colours
and Fonts
grid The Grid Graphics Package
GSEABase Gene set enrichment data structures and methods
hgu133a Affymetrix Human Genome U133 Set Annotation
Data (hgu133a)
hgu95av2 Affymetrix Human Genome U95 Set Annotation Data
(hgu95av2)
hgu95av2.db Affymetrix Human Genome U95 Set annotation data
(chip hgu95av2)
hgu95av2cdf hgu95av2cdf
KEGG A data package containing annotation data for
KEGG
keggorth graph support for KO, KEGG Orthology
KernSmooth Functions for kernel smoothing for Wand & Jones
(1995)
lattice Lattice Graphics
limma Linear Models for Microarray Data
makecdfenv CDF Environment Maker
MAQCsubset Experimental Data Package: MAQCsubset
marray Exploratory analysis for two-color spotted
microarray data
MASS Main Package of Venables and Ripley's MASS
matchprobes Tools for sequence matching of probes on arrays
Matrix A Matrix package for R
methods Formal Methods and Classes
mgcv GAMs with GCV smoothness estimation and GAMMs
by REML/PQL
MLInterfaces Uniform interfaces to R machine learning
procedures for data in Bioconductor containers
multtest Resampling-based multiple hypothesis testing
Neve2006 expression and CGH data on breast cancer cell
lines
nlme Linear and Nonlinear Mixed Effects Models
nnet Feed-forward Neural Networks and Multinomial
Log-Linear Models
pamr Pam: prediction analysis for microarrays
ppiData A package that contains the bait to prey
directed graphs for protein-protein
interactions.
preprocessCore A collection of pre-processing functions
R.matlab Read and write of MAT files together with
R-to-Matlab connectivity
R.oo R object-oriented programming with or without
references
randomForest Breiman and Cutler's random forests for
classification and regression
RBGL Interface to boost C++ graph lib
RColorBrewer ColorBrewer palettes
rcompgen Completion generator for R
RCurl HTTP request interface
rda Shrunken Centroids Regularized Discriminant
Analysis
Rgraphviz Provides plotting capabilities for R graph
objects
ROC utilities for ROC, with uarray focus
rpart Recursive Partitioning
RSQLite SQLite interface for R
siggenes Multiple testing using SAM and Efron's
empirical Bayes approaches
simpleaffy Very simple high level analysis of Affymetrix
data
sma Statistical Microarray Analysis
spatial Functions for Kriging and Point Pattern
Analysis
splines Regression Spline Functions and Classes
statmod Statistical Modeling
stats The R Stats Package
stats4 Statistical Functions using S4 Classes
survival Survival analysis, including penalised
likelihood.
tcltk Tcl/Tk Interface
tkWidgets R based tk widgets
tools Tools for Package Development
utils The R Utils Package
vsn Variance stabilization and calibration for
microarray data
widgetTools Creates an interactive tcltk widget
XML Tools for parsing and generating XML within R
and S-Plus.
xtable Export tables to LaTeX or HTML
yeastExpData Yeast Experimental Data
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