Package | Title |
Version |
aCGH |
Classes and functions for Array Comparative Genomic
Hybridization data. |
1.1.7 |
affy |
Methods for Affymetrix Oligonucleotide Arrays |
1.6.7 |
affycomp |
Graphics Toolbox for Assessment of Affymetrix Expression
Measures |
1.4.3 |
affydata |
Affymetrix Data for Demonstration Purpose |
1.4.1 |
affylmGUI |
GUI for affy analysis using limma package |
1.2.7 |
affypdnn |
Probe Dependent Nearest Neighbours (PDNN) for the affy package |
1.1.0 |
affyPLM |
Methods for fitting probe-level models |
1.3.3 |
altcdfenvs |
alternative cdfenvs |
1.1.11 |
annaffy |
Annotation tools for Affymetrix biological metadata |
1.0.18 |
AnnBuilder |
Bioconductor annotation data package builder |
1.5.30 |
annotate |
Annotation for microarrays |
1.5.9 |
apComplex |
Estimate protein complex membership using AP-MS protein data |
1.1.5 |
arrayMagic |
two-colour cDNA array quality control and preprocessing |
1.5.8 |
arrayQuality |
Assessing array quality on spotted arrays |
1.0.11 |
bim |
Bayesian Interval Mapping Diagnostics |
1.0.3 |
Biobase |
Biobase: Base functions for Bioconductor |
1.5.12 |
bioDist |
Different distance measures |
1.0.0 |
biomaRt |
Interface to BioMart databases (e.g. Ensembl) |
1.0.4 |
Biostrings |
String objects reepresenting biological sequences |
1.1.1 |
bridge |
Bayesian Robust Inference for Differential Gene Expression |
1.0.1 |
Category |
Category Analysis |
1.0.1 |
ChromoViz |
Multimodal visualization of gene expression |
1.0 |
CoCiteStats |
Different test statistics based on co-citation. |
1.0.0 |
convert |
Convert Microarray Data Objects |
1.1.11 |
ctc |
Cluster and Tree Conversion. |
1.2.7 |
daMA |
Efficient design and analysis of factorial two-colour
microarray data |
1.0.1 |
DEDS |
Differential Expression via Distance Summary for Microarray
Data |
1.0.5 |
DNAcopy |
DNA copy number data analysis |
1.1.2 |
DynDoc |
Dynamic document tools |
1.5.5 |
EBarrays |
Empirical Bayes for Microarrays |
1.0.19 |
ecolitk |
Meta-data and tools for E. coli |
1.0.1 |
edd |
expression density diagnostics |
1.5.1 |
factDesign |
Factorial designed microarray experiment analysis |
1.1.5 |
gcrma |
Background Adjustment Using Sequence Information |
1.1.3 |
genArise |
Microarray Analysis tool |
1.3.2 |
genefilter |
genefilter: filter genes |
1.6.1 |
GeneMeta |
MetaAnalysis for High Throughput Experiments |
1.0.0 |
geneplotter |
Grapics related functions for Bioconductor |
1.6.1 |
GeneR |
R for genes and sequences analysis |
1.0.0 |
geneRecommender |
A gene recommender algorithm to identify genes coexpressed with
a query set of genes |
1.0.2 |
GeneSpring |
GeneSpring R Integration Functions |
2.0.0 |
GeneTraffic |
GeneTraffic R Integration Functions |
1.0.6 |
GeneTS |
Microarray Time Series and Network Analysis |
2.4.1 |
GLAD |
Gain and Loss Analysis of DNA |
1.0.4 |
globaltest |
Testing Association of a Group of Genes with a Clinical
Variable |
3.0.5 |
goCluster |
Analysis of clustering results in conjunction with annotation
data. |
1.0.3 |
GOstats |
Tools for manipulating GO and microarrays. |
1.1.3 |
goTools |
Functions for Gene Ontology database |
1.0.6 |
gpls |
Classification using generalized partial least squares |
1.0.6 |
graph |
graph: A package to handle graph data structures |
1.5.9 |
GraphAT |
Graph Theoretic Association Tests |
1.0.0 |
hexbin |
Hexagonal Binning Routines |
1.2-1 |
hopach |
Hierarchical Ordered Partitioning and Collapsing Hybrid
(HOPACH) |
1.1.1 |
hypergraph |
A package providing hypergraph data structures |
1.0.0 |
Icens |
NPMLE for Censored and Truncated Data |
1.0.0 |
ideogram |
ideogram |
1.0.0 |
impute |
impute: Imputation for microarray data |
1.0.2 |
iSPlot |
Linking Plots |
1.0.7 |
KEGGSOAP |
Client-side SOAP access KEGG |
1.1.1 |
limma |
Linear Models for Microarray Data |
1.9.6 |
limmaGUI |
GUI for limma package |
1.3.9 |
LPE |
Methods for analyzing microarray data using Local Pooled Error
(LPE) method |
1.1.5 |
macat |
MicroArray Chromosome Analysis Tool |
1.2.0 |
made4 |
Multivariate analysis of microarray data using ADE4 |
1.0.0 |
makecdfenv |
CDF Environment Maker |
1.5.1 |
marray |
Exploratory analysis for two-color spotted microarray data |
1.6.3 |
matchprobes |
Tools for sequence matching of probes on arrays |
1.0.17 |
MCRestimate |
Misclassification error estimation with cross-validation |
1.2.6 |
MeasurementError.cor |
Measurement Error model estimate for correlation coefficient |
1.0.2 |
MergeMaid |
Merge Maid |
2.0.1 |
MiPP |
MiPP (Misclassification Penalized Posterior)-based
Classification |
1.0.2 |
MLInterfaces |
MLInterfaces |
1.0.10 |
msbase |
Basic classes and methods for mass spectrometric mass list
manipulation. |
1.1.1 |
mscalib |
Calibration and filtering of mass spectrometric peak(mass)
lists. |
1.0.1 |
multtest |
Resampling-based multiple hypothesis testing |
1.6.0 |
nnNorm |
Spatial and intensity based normalization of cDNA microarray
data based on robust neural nets |
1.1.0 |
OLIN |
Optimized local intensity-dependent normalisation of two-color
microarrays |
1.3.3 |
OLINgui |
Graphical user interface for OLIN |
1.0.1 |
ontoTools |
graphs and sparse matrices for working with ontologies; formal
objects for nomenclatures with provenance management |
1.4.8 |
pairseqsim |
pairwise sequence alignment similarity simple. |
1.0.4 |
pamr |
Pam: prediction analysis for microarrays |
1.22 |
pickgene |
Adaptive Gene Picking for Microarray Expression Data Analysis |
1.0.0 |
plgem |
Power Law Global Error Model |
1.0.0 |
plier |
Implements the Affymetrix PLIER algorithm |
1.0.0 |
prada |
Data analysis for cell-based functional assays |
1.3.1 |
PROcess |
Ciphergen SELDI-TOF Processing |
1.3.4 |
qvalue |
Q-value estimation for false discovery rate control |
1.1.0 |
rama |
Robust Analysis of MicroArrays |
1.0.1 |
RankProd |
Rank Product method for identifying differentially expressed
genes. |
1.0.0 |
Rdbi |
Generic database methods |
1.1.2 |
reposTools |
Repository tools for R |
1.5.19 |
Resourcerer |
Reads annotation data from TIGR Resourcerer or convert the
annotation data into Bioconductor data pacakge. |
1.1.0 |
rflowcyt |
Statistical tools and data structures for analytic flow
cytometry |
1.0.0 |
RMAGEML |
Handling MAGEML documents |
2.1.0 |
ROC |
utilities for ROC, with uarray focus |
1.1.1 |
RSNPper |
interface to chip.org::SNPper for SNP-related data |
1.0.5 |
Ruuid |
Ruuid: Provides Universally Unique ID values |
1.5.2 |
safe |
Significance Analysis of Function and Expression |
1.0.0 |
SAGElyzer |
A package that deals with SAGE libraries |
1.5.1 |
sagenhaft |
Collection of functions for reading and comparing SAGE
libraries |
1.0.0 |
siggenes |
SAM and Efron's empirical Bayes approaches |
1.2.17 |
simpleaffy |
Very simple high level analysis of Affymetrix data |
2.0.12 |
SNAData |
Social Networks Analysis Data Examples |
1.1.1 |
splicegear |
splicegear |
1.0.10 |
spotSegmentation |
Microarray Spot Segmentation and Gridding for Blocks of
Microarray Spots |
1.1.1 |
ssize |
Estimate Microarry Sample Size |
1.0.1 |
stam |
Structured Analysis of Microarray Data |
1.0.9 |
stepNorm |
Stepwise normalization functions for cDNA microarrays |
1.0.2 |
tilingArray |
Analysis of tiling arrays |
1.0.1 |
tkWidgets |
R based tk widgets |
1.5.23 |
twilight |
Estimation of local false discovery rate |
1.1.0 |
vsn |
Variance stabilization and calibration for microarray data |
1.6.3 |
webbioc |
Bioconductor Web Interface |
1.0.1 |
widgetInvoke |
Evaluation widgets for functions |
1.0.0 |
widgetTools |
Creates an interactive tcltk widget |
1.4.7 |
xcms |
LC/MS and GC/MS Data Analysis |
1.0.0 |