Package |
Maintainer |
Title |
ABarray
|
Yongming Andrew Sun |
Microarray QA and statistical data analysis for Applied
Biosystems Genome Survey Micorarray (AB1700) gene expression
data. |
aCGH
|
Jane Fridlyand |
Classes and functions for Array Comparative Genomic
Hybridization data. |
ACME
|
Sean Davis |
Algorithms for Calculating Microarray Enrichment (ACME) |
adSplit
|
Claudio Lottaz |
Annotation-Driven Clustering |
affxparser
|
Kasper Daniel Hansen |
Affymetrix File Parsing SDK |
affy
|
Rafael A. Irizarry |
Methods for Affymetrix Oligonucleotide Arrays |
affycomp
|
Rafael A. Irizarry |
Graphics Toolbox for Assessment of Affymetrix Expression
Measures |
AffyCompatible
|
Martin Morgan |
Affymetrix GeneChip software compatibility |
affyContam
|
V. Carey |
structured corruption of affymetrix cel file data |
affycoretools
|
James W. MacDonald |
Functions useful for those doing repetitive analyses with
Affymetrix GeneChips. |
AffyExpress
|
Xuejun Arthur Li |
Affymetrix Quality Assessment and Analysis Tool |
affyio
|
Benjamin Milo Bolstad |
Tools for parsing Affymetrix data files |
affylmGUI
|
Keith Satterley |
GUI for affy analysis using limma package |
affyPara
|
Markus Schmidberger |
Parallelized preprocessing methods for Affymetrix
Oligonucleotide Arrays |
affypdnn
|
Laurent Gautier |
Probe Dependent Nearest Neighbours (PDNN) for the affy package |
affyPLM
|
Ben Bolstad |
Methods for fitting probe-level models |
affyQCReport
|
Craig Parman |
QC Report Generation for affyBatch objects |
AffyTiling
|
Charles G. Danko |
Easy extraction of individual probes in Affymetrix tiling arrays |
Agi4x44PreProcess
|
Pedro Lopez-Romero |
PreProcessing of Agilent 4x44 array data |
altcdfenvs
|
Laurent Gautier |
alternative CDF environments (aka probeset mappings) |
annaffy
|
Colin A. Smith |
Annotation tools for Affymetrix biological metadata |
annotate
|
Biocore Team c/o BioC user list
|
Annotation for microarrays |
AnnotationDbi
|
Biocore Team c/o BioC user list
|
Annotation Database Interface |
annotationTools
|
Alexandre Kuhn |
Annotate microarrays and perform cross-species gene expression
analyses using flat file databases. |
apComplex
|
Denise Scholtens |
Estimate protein complex membership using AP-MS protein data |
aroma.light
|
Henrik Bengtsson |
Light-weight methods for normalization and visualization of
microarray data using only basic R data types |
ArrayExpress
|
Audrey Kauffmann |
Access the ArrayExpress Microarray Database at EBI and build
Bioconductor data structures: ExpressionSet, AffyBatch,
NChannelSet |
arrayMvout
|
V. Carey |
multivariate outlier detection for expression array QA |
arrayQuality
|
Agnes Paquet |
Assessing array quality on spotted arrays |
arrayQualityMetrics
|
Audrey Kauffmann |
Quality metrics on microarray data sets |
ArrayTools
|
Arthur Li |
geneChip Analysis Package |
BAC
|
Raphael Gottardo |
Bayesian Analysis of Chip-chip experiment |
BCRANK
|
Adam Ameur |
Predicting binding site consensus from ranked DNA sequences |
beadarray
|
Mark Dunning |
Quality assessment and low-level analysis for Illumina BeadArray
data |
beadarraySNP
|
Jan Oosting |
Normalization and reporting of Illumina SNP bead arrays |
betr
|
Martin Aryee |
Identify differentially expressed genes in microarray
time-course data |
bgafun
|
Iain Wallace |
BGAfun A method to identify specifity determining residues in
protein families |
BGmix
|
Alex Lewin |
Bayesian models for differential gene expression |
bgx
|
Ernest Turro |
Bayesian Gene eXpression |
BicARE
|
Pierre Gestraud |
Biclustering Analysis and Results Exploration |
Biobase
|
Biocore Team c/o BioC user list
|
Biobase: Base functions for Bioconductor |
BiocCaseStudies
|
Biocore Team c/o BioC user list
|
BiocCaseStudies: Support for the Case Studies Monograph |
biocDatasets
|
L. Gautier |
Synthetic datasets for bioconductor |
biocGraph
|
Florian Hahne |
Graph examples and use cases in Bioinformatics |
biocViews
|
Biocore Team c/o BioC user list
|
Categorized views of R package repositories |
bioDist
|
Biocore Team c/o BioC user list
|
Different distance measures |
biomaRt
|
Steffen Durinck |
Interface to BioMart databases (e.g. Ensembl, Wormbase and
Gramene) |
BioMVCClass
|
Elizabeth Whalen |
Model-View-Controller (MVC) Classes That Use Biobase |
Biostrings
|
H. Pages |
String objects representing biological sequences, and matching
algorithms |
bridge
|
Raphael Gottardo |
Bayesian Robust Inference for Differential Gene Expression |
BSgenome
|
H. Pages |
Infrastructure for Biostrings-based genome data packages |
BufferedMatrix
|
Benjamin Milo Bolstad |
A matrix data storage object held in temporary files |
BufferedMatrixMethods
|
B. M. Bolstad |
Microarray Data related methods that utlize BufferedMatrix
objects |
CALIB
|
Hui Zhao |
Calibration model for estimating absolute expression levels from
microarray data |
CAMERA
|
Carsten Kuhl |
Collection of annotation related methods for mass spectrometry
data |
Category
|
Robert Gentleman |
Category Analysis |
cellHTS
|
Ligia Bras |
Analysis of cell-based screens |
cellHTS2
|
Florian Hahne |
Analysis of cell-based screens - revised version of cellHTS |
CGHbase
|
Sjoerd Vosse |
CGHbase: Base functions and classes for arrayCGH data analysis. |
CGHcall
|
Sjoerd Vosse |
Calling aberrations for array CGH tumor profiles. |
cghMCR
|
J. Zhang |
Find chromosome regions showing common gains/losses |
CGHregions
|
Sjoerd Vosse |
Dimension Reduction for Array CGH Data with Minimal Information
Loss. |
ChemmineR
|
Y. Eddie Cao |
A Compound Data Mining Framework |
clusterStab
|
James W. MacDonald |
Compute cluster stability scores for microarray data |
CMA
|
Martin Slawski |
Synthesis of microarray-based classification |
CoCiteStats
|
R. Gentleman |
Different test statistics based on co-citation. |
codelink
|
Diego Diez |
Manipulation of Codelink Bioarrays data. |
convert
|
Yee Hwa (Jean) Yang |
Convert Microarray Data Objects |
copa
|
James W. MacDonald |
Functions to perform cancer outlier profile analysis. |
CORREP
|
Dongxiao Zhu |
Multivariate Correlation Estimator and Statistical Inference
Procedures. |
cosmo
|
Oliver Bembom |
Supervised detection of conserved motifs in DNA sequences |
cosmoGUI
|
Oliver Bembom |
GUI for constructing constraint sets used by the cosmo package |
crlmm
|
Benilton S Carvalho , Robert Scharpf
, Matt Ritchie |
Genotype Calling (CRLMM) and Copy Number Analysis tool for
Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
ctc
|
Antoine Lucas |
Cluster and Tree Conversion. |
daMA
|
Jobst Landgrebe |
Efficient design and analysis of factorial two-colour microarray
data |
DAVIDQuery
|
Roger Day |
Retrieval from the DAVID bioinformatics data resource into R |
DEDS
|
Yuanyuan Xiao |
Differential Expression via Distance Summary for Microarray Data |
DFP
|
Rodrigo Alvarez-Glez |
Gene Selection |
diffGeneAnalysis
|
Choudary Jagarlamudi |
Performs differential gene expression Analysis |
DNAcopy
|
Venkatraman E. Seshan |
DNA copy number data analysis |
domainsignatures
|
Florian Hahne |
Geneset enrichment based on InterPro domain signatures |
dualKS
|
Eric J. Kort |
Dual KS Discriminant Analysis and Classification |
dyebias
|
Philip Lijnzaad |
Methods to correct for gene-specific dye bias |
DynDoc
|
Biocore Team c/o BioC user list
|
Dynamic document tools |
EBarrays
|
Ming Yuan |
Unified Approach for Simultaneous Gene Clustering and
Differential Expression Identification |
EBImage
|
Gregoire Pau |
Image processing toolbox for R |
ecolitk
|
Laurent |
Meta-data and tools for E. coli |
edd
|
Vince Carey |
expression density diagnostics |
edgeR
|
Mark Robinson , Davis McCarthy
|
Empirical analysis of digital gene expression data in R |
exonmap
|
Crispin Miller |
High level analysis of Affymetrix exon array data |
explorase
|
Michael Lawrence |
GUI for exploratory data analysis of systems biology data |
externalVector
|
Biocore Team c/o BioC user list
|
Vector objects for R with external storage |
factDesign
|
Denise Scholtens |
Factorial designed microarray experiment analysis |
fbat
|
The R Genetics Project
|
Family Based Association Tests for genetic data. |
fdrame
|
Effi Kenigsberg |
FDR adjustments of Microarray Experiments (FDR-AME) |
flagme
|
Mark Robinson |
Analysis of Metabolomics GC/MS Data |
flowClust
|
Raphael Gottardo |
Clustering for Flow Cytometry |
flowCore
|
F. Hahne |
flowCore: Basic structures for flow cytometry data |
flowFlowJo
|
John J. Gosink |
Tools for extracting information from a FlowJo workspace and
working with the data in the flowCore paradigm. |
flowQ
|
F. Hahne |
Qualitiy control for flow cytometry |
flowStats
|
Florian Hahne |
Statistical methods for the analysis of flow cytometry data |
flowUtils
|
Nishant Gopalakrishnan |
Utilities for flow cytometry |
flowViz
|
Florian Hahne |
Visualization for flow cytometry |
gaga
|
David Rossell |
GaGa hierarchical model for microarray data analysis |
gaggle
|
Dan Tenenbaum |
Broadcast data between R and other bioinformatics programs |
gcrma
|
Z. Wu |
Background Adjustment Using Sequence Information |
genArise
|
IFC Development Team |
Microarray Analysis tool |
gene2pathway
|
Holger Froehlich |
Prediction of KEGG pathway membership for individual genes based
on InterPro domain signatures |
genefilter
|
Biocore Team c/o BioC user list
|
genefilter: methods for filtering genes from microarray
experiments |
GeneMeta
|
Biocore Team c/o BioC user list
|
MetaAnalysis for High Throughput Experiments |
geneplotter
|
Biocore Team c/o BioC user list
|
Graphics related functions for Bioconductor |
GeneR
|
Y. d'Aubenton-Carafa |
R for genes and sequences analysis |
geneRecommender
|
Greg Hather |
A gene recommender algorithm to identify genes coexpressed with
a query set of genes |
GeneRegionScan
|
Lasse Folkersen |
GeneRegionScan |
GeneRfold
|
Antoine Lucas |
R for genes and sequences, using viennaRNA package (fold) |
GeneSelectMMD
|
Weiliang Qiu |
Gene selection based on the marginal distributions of gene
profiles that characterized by a mixture of three-component
multivariate distributions |
GeneSelector
|
Martin Slawski |
GeneSelector |
GeneSpring
|
Thon de Boer |
GeneSpring R Integration Functions |
GeneticsBase
|
The R Genetics Project
|
Classes and functions for handling genetic data |
GeneticsDesign
|
The R Genetics Project
|
Functions for designing genetics studies |
GeneticsPed
|
The R Genetics Project
|
Pedigree and genetic relationship functions |
GeneTraffic
|
Daniel Iordan |
GeneTraffic R Integration Functions |
GenomeGraphs
|
Steffen Durinck |
Plotting genomic information from Ensembl |
genomeIntervals
|
Julien Gagneur |
Operations on genomic intervals |
GEOmetadb
|
Jack Zhu |
A compilation of metadata from NCBI GEO |
GEOquery
|
Sean Davis |
Get data from NCBI Gene Expression Omnibus (GEO) |
GGBase
|
Vince Carey |
infrastructure for genetics of gene expression (c) 2008 VJ Carey |
GGtools
|
Vince Carey |
software and data for genetical genomics (c) 2006 VJ Carey |
GLAD
|
Philippe Hupe |
Gain and Loss Analysis of DNA |
GlobalAncova
|
R. Meister |
Calculates a global test for differential gene expression
between groups |
globaltest
|
Jelle Goeman |
Testing Association of Groups of Genes with a Clinical Variable |
goProfiles
|
Alex Sanchez |
goProfiles: an R package for the statistical analysis of
functional profiles |
GOSemSim
|
Guangchuang Yu |
GO-terms Semantic Similarity Measures |
GOstats
|
Robert Gentleman |
Tools for manipulating GO and microarrays. |
goTools
|
Agnes Paquet |
Functions for Gene Ontology database |
gpls
|
Biocore Team c/o BioC user list
|
Classification using generalized partial least squares |
graph
|
Robert Gentleman |
graph: A package to handle graph data structures |
GraphAlignment
|
Joern P. Meier |
GraphAlignment |
GraphAT
|
Thomas LaFramboise |
Graph Theoretic Association Tests |
GSEABase
|
Biocore Team c/o BioC user list
|
Gene set enrichment data structures and methods |
GSEAlm
|
Assaf Oron |
Linear Model Toolset for Gene Set Enrichment Analysis |
Harshlight
|
Maurizio Pellegrino |
A "corrective make-up" program for microarray chips |
Heatplus
|
Alexander Ploner |
A heat map displaying covariates and coloring clusters |
HELP
|
Reid F. Thompson |
Tools for HELP data analysis |
HEM
|
HyungJun Cho |
Heterogeneous error model for identification of differentially
expressed genes under multiple conditions |
hexbin
|
Nicholas Lewin-Koh |
Hexagonal Binning Routines |
HilbertVis
|
Simon Anders |
Hilbert curve visualization |
HilbertVisGUI
|
Simon Anders |
HilbertVisGUI |
hopach
|
Katherine S. Pollard |
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
hypergraph
|
Robert Gentleman |
A package providing hypergraph data structures |
Icens
|
Biocore Team c/o BioC user list
|
NPMLE for Censored and Truncated Data |
idiogram
|
Karl J. Dykema |
idiogram |
impute
|
Balasubramanian Narasimhan |
impute: Imputation for microarray data |
IRanges
|
Biocore Team c/o BioC user list
|
Infrastructure for manipulating intervals on sequences |
ITALICS
|
Guillem Rigaill |
ITALICS |
iterativeBMA
|
Ka Yee Yeung |
The Iterative Bayesian Model Averaging (BMA) algorithm |
iterativeBMAsurv
|
Ka Yee Yeung |
The Iterative Bayesian Model Averaging (BMA) Algorithm For
Survival Analysis |
KCsmart
|
Jorma de Ronde |
Multi sample aCGH analysis package using kernel convolution |
KEGGgraph
|
Jitao David Zhang |
KEGGgraph: A graph approach to KEGG PATHWAY in R and
Bioconductor |
keggorth
|
VJ Carey |
graph support for KO, KEGG Orthology |
KEGGSOAP
|
Robert Gentleman |
Client-side SOAP access KEGG |
lapmix
|
Yann Ruffieux |
Laplace Mixture Model in Microarray Experiments |
LBE
|
Cyril Dalmasso |
Estimation of the false discovery rate. |
limma
|
Gordon Smyth |
Linear Models for Microarray Data |
limmaGUI
|
Keith Satterley |
GUI for limma package |
LMGene
|
John Tillinghast |
LMGene Software for Date Transformation and Identification of
Differentially Expressed Genes in Gene Expression Arrays |
logicFS
|
Holger Schwender |
Identification of SNP Interactions |
logitT
|
Tobias Guennel |
logit-t Package |
LPE
|
Nitin Jain |
Methods for analyzing microarray data using Local Pooled Error
(LPE) method |
LPEadj
|
Carl Murie |
A correction of the local pooled error (LPE) method to replace
the asymptotic variance adjustment with an unbiased adjustment
based on sample size. |
lumi
|
Pan Du |
BeadArray Specific Methods for Illumina Microarrays |
maanova
|
Keith Sheppard |
Tools for analyzing Micro Array experiments |
macat
|
Joern Toedling |
MicroArray Chromosome Analysis Tool |
maCorrPlot
|
Alexander Ploner |
Visualize artificial correlation in microarray data |
maDB
|
Johannes Rainer |
Microarray database and utility functions for microarray data
analysis. |
made4
|
Aedin Culhane |
Multivariate analysis of microarray data using ADE4 |
maigesPack
|
Gustavo H. Esteves |
Functions to handle cDNA microarray data, including several
methods of data analysis |
makecdfenv
|
James W. MacDonald |
CDF Environment Maker |
makePlatformDesign
|
Benilton Carvalho |
Platform Design Package |
MANOR
|
Pierre Neuvial |
CGH Micro-Array NORmalization |
MantelCorr
|
Brian Steinmeyer |
Compute Mantel Cluster Correlations |
marray
|
Yee Hwa (Jean) Yang |
Exploratory analysis for two-color spotted microarray data |
maSigPro
|
Ana Conesa |
Significant Gene Expression Profile Differences in Time Course
Microarray Data |
MassSpecWavelet
|
Pan Du |
Mass spectrum processing by wavelet-based algorithms |
matchprobes
|
Biocore Team c/o BioC user list
|
Basic infrastructure for using oligonucleotide microarray
reporter sequence information for preprocessing and quality
assessment |
MCRestimate
|
Marc Johannes |
Misclassification error estimation with cross-validation |
mdqc
|
Gabriela Cohen-Freue |
Mahalanobis Distance Quality Control for microarrays |
MeasurementError.cor
|
Beiying Ding |
Measurement Error model estimate for correlation coefficient |
MEDME
|
Mattia Pelizzola |
Modelling Experimental Data from MeDIP Enrichment |
MergeMaid
|
Xiaogang Zhong |
Merge Maid |
metaArray
|
Hyungwon Choi |
Integration of Microarray Data for Meta-analysis |
metahdep
|
John R. Stevens |
Hierarchical Dependence in Meta-Analysis |
Mfuzz
|
Matthias Futschik |
Soft clustering of time series gene expression data |
microRNA
|
Robert Gentleman |
Data and functions for dealing with microRNAs |
minet
|
Patrick E. Meyer |
Mutual Information Network Inference |
MiPP
|
Sukwoo Kim |
Misclassification Penalized Posterior Classification |
miRNApath
|
James M. Ward |
miRNApath: Pathway Enrichment for miRNA Expression Data |
MLInterfaces
|
V. Carey |
Uniform interfaces to R machine learning procedures for data in
Bioconductor containers |
multiscan
|
Mizanur Khondoker |
R package for combining multiple scans |
multtest
|
Katherine S. Pollard |
Resampling-based multiple hypothesis testing |
MVCClass
|
Elizabeth Whalen |
Model-View-Controller (MVC) Classes |
nem
|
Christian Bender |
Nested Effects Models to reconstruct phenotypic hierarchies |
nnNorm
|
Adi Laurentiu Tarca |
Spatial and intensity based normalization of cDNA microarray
data based on robust neural nets |
nudge
|
N. Dean |
Normal Uniform Differential Gene Expression detection |
occugene
|
Oliver Will |
Functions for Multinomial Occupancy Distribution |
OCplus
|
Alexander Ploner |
Operating characteristics plus sample size and local fdr for
microarray experiments |
oligo
|
Benilton Carvalho |
Tools for low-level analysis of oligonucleotide arrays. |
oligoClasses
|
Benilton Carvalho |
Classes for high-throughput SNP arrays |
OLIN
|
Matthias Futschik |
Optimized local intensity-dependent normalisation of two-color
microarrays |
OLINgui
|
Matthias Futschik |
Graphical user interface for OLIN |
oneChannelGUI
|
Raffaele A Calogero |
This package extends the capabilities of affylmGUI graphical
interface. Affymetrix 3' IVT, gene an exon arrays are actually
implemented togheter with Illumina, GEO matrix series files and
tab delimited files. |
ontoTools
|
Vince Carey |
graphs and sparse matrices for working with ontologies; formal
objects for nomenclatures with provenance management |
OrderedList
|
Claudio Lottaz |
Similarities of Ordered Gene Lists |
OutlierD
|
Sukwoo Kim |
Outlier detection using quantile regression on the M-A
scatterplots of high-throughput data |
pamr
|
Rob Tibshirani |
Pam: prediction analysis for microarrays |
PAnnBuilder
|
Li Hong |
Protein annotation data package builder |
panp
|
Peter Warren |
Presence-Absence Calls from Negative Strand Matching Probesets |
parody
|
VJ Carey |
Parametric And Resistant Outlier DYtection |
pathRender
|
Li Long |
Render molecular pathways |
pcaMethods
|
Wolfram Stacklies |
A collection of PCA methods. |
pcot2
|
Sarah Song |
Principal Coordinates and Hotelling's T-Square method |
PCpheno
|
Nolwenn Le Meur |
Phenotypes and cellular organizational units |
pdInfoBuilder
|
Benilton Carvalho |
Platform Design Information Package Builder |
pdmclass
|
James W. MacDonald |
Classification of Microarray Samples using Penalized
Discriminant Methods |
PGSEA
|
Karl Dykema |
Parametric Gene Set Enrichment Analysis |
pgUtils
|
Johannes Rainer |
Utility functions for PostgreSQL databases |
pickgene
|
Brian S. Yandell |
Adaptive Gene Picking for Microarray Expression Data Analysis |
pkgDepTools
|
Seth Falcon |
Package Dependency Tools |
plgem
|
Norman Pavelka |
Power Law Global Error Model |
plier
|
Crispin Miller |
Implements the Affymetrix PLIER algorithm |
PLPE
|
Soo-heang Eo |
Local Pooled Error Test for Differential Expression with Paired
High-throughput Data |
plw
|
Magnus Astrand |
Probe level Locally moderated Weighted t-tests. |
ppiStats
|
Tony Chiang |
Protein-Protein Interaction Statistical Package |
prada
|
Florian Hahne |
Data analysis for cell-based functional assays |
preprocessCore
|
Benjamin Milo Bolstad |
A collection of pre-processing functions |
PROcess
|
Xiaochun Li |
Ciphergen SELDI-TOF Processing |
puma
|
Richard Pearson |
Propagating Uncertainty in Microarray Analysis |
qpcrNorm
|
Jessica Mar |
Data-driven normalization strategies for high-throughput qPCR
data. |
qpgraph
|
Robert Castelo |
Reverse engineering of molecular regulatory networks with
qp-graphs |
quantsmooth
|
Jan Oosting |
Quantile smoothing and genomic visualization of array data |
qvalue
|
John D. Storey |
Q-value estimation for false discovery rate control |
rama
|
Raphael Gottardo |
Robust Analysis of MicroArrays |
RankProd
|
Fangxin Hong |
Rank Product method for identifying differentially expressed
genes with application in meta-analysis |
RbcBook1
|
Vince Carey |
Support for Springer monograph on Bioconductor |
RBGL
|
Li Long |
An interface to the BOOST graph library |
RBioinf
|
Robert Gentleman |
RBioinf |
rbsurv
|
Soo-heang Eo |
Robust likelihood-based survival modeling with microarray data |
Rdbi
|
Jianhua Zhang |
Generic database methods |
RdbiPgSQL
|
Jianhua Zhang |
PostgreSQL access |
Rdisop
|
Steffen Neumann |
Decomposition of Isotopic Patterns |
reb
|
Karl J. Dykema |
Regional Expression Biases |
RefPlus
|
Kai-Ming Chang |
A function set for the Extrapolation Strategy (RMA+) and
Extrapolation Averaging (RMA++) methods. |
Resourcerer
|
Jianhua Zhang |
Reads annotation data from TIGR Resourcerer or convert the
annotation data into Bioconductor data pacakge. |
rflowcyt
|
N. LeMeur |
Statistical tools and data structures for analytic flow
cytometry |
Rgraphviz
|
Kasper Hansen |
Provides plotting capabilities for R graph objects |
rHVDM
|
Martino Barenco |
Hidden Variable Dynamic Modeling |
Ringo
|
J. Toedling |
R Investigation of ChIP-chip Oligoarrays |
Rintact
|
Tony Chiang |
Interface to EBI Intact protein interaction data base |
RLMM
|
Nusrat Rabbee |
A Genotype Calling Algorithm for Affymetrix SNP Arrays |
RMAGEML
|
Steffen Durinck |
Handling MAGEML documents |
Rmagpie
|
Camille Maumet |
MicroArray Gene-expression-based Program In Error rate
estimation |
rMAT
|
Arnaud Droit and Raphael Gottardo
|
R implementation from MAT program to normalize and analyze
tiling arrays and ChIP-chip data. |
RNAither
|
Nora Rieber |
Statistical analysis of high-throughput RNAi screens |
ROC
|
Vince Carey |
utilities for ROC, with uarray focus |
RpsiXML
|
Jitao David Zhang |
R interface to PSI-MI 2.5 files |
Rredland
|
VJ Carey |
interface to redland RDF utilities |
rsbml
|
Michael Lawrence |
R support for SBML, using libsbml |
rtracklayer
|
Michael Lawrence |
R interface to genome browsers and their annotation tracks |
Rtreemix
|
Jasmina Bogojeska |
Rtreemix: Mutagenetic trees mixture models. |
Ruuid
|
Biocore Team c/o BioC user list
|
Ruuid: Provides Universally Unique ID values |
RWebServices
|
Martin Morgan |
Expose R functions as web services through Java/Axis/Apache |
safe
|
William T. Barry |
Significance Analysis of Function and Expression |
sagenhaft
|
Tim Beissbarth |
Collection of functions for reading and comparing SAGE libraries |
SAGx
|
Per Broberg, |
Statistical Analysis of the GeneChip |
SBMLR
|
Tomas Radivoyevitch |
SBML-R Interface and Analysis Tools |
ScISI
|
Tony Chiang |
In Silico Interactome |
seqLogo
|
Oliver Bembom |
Sequence logos for DNA sequence alignments |
ShortRead
|
Biocore Team c/o BioC user list
|
Base classes and methods for high-throughput short-read
sequencing data. |
siggenes
|
Holger Schwender |
Multiple testing using SAM and Efron's empirical Bayes
approaches |
sigPathway
|
Weil Lai |
Pathway Analysis |
SIM
|
Maarten van Iterson |
Integrated Analysis of gene expression and copynumber data |
simpleaffy
|
Crispin Miller |
Very simple high level analysis of Affymetrix data |
simulatorAPMS
|
Tony Chiang |
Computationally simulates the AP-MS technology. |
sizepower
|
Weiliang Qiu |
Sample Size and Power Calculation in Micorarray Studies |
SLGI
|
Nolwenn Le Meur |
Synthetic Lethal Genetic Interaction |
SLqPCR
|
Matthias Kohl |
Functions for analysis of real-time quantitative PCR data at
SIRS-Lab GmbH |
SMAP
|
Robin Andersson |
A Segmental Maximum A Posteriori Approach to Array-CGH Copy
Number Profiling |
snapCGH
|
John Marioni |
Segmentation, normalisation and processing of aCGH data. |
SNPchip
|
Robert Scharpf |
Classes and Methods for high throughput SNP chip data |
snpMatrix
|
David Clayton |
The snp.matrix and X.snp.matrix classes |
SPIA
|
Adi Laurentiu Tarca |
Signaling Pathway Impact Analysis (SPIA) using combined evidence
of pathway over-representation and unusual signaling
perturbations |
spikeLI
|
Enrico Carlon |
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
spkTools
|
Matthew N McCall |
Methods for Spike-in Arrays |
splicegear
|
Laurent Gautier |
splicegear |
splots
|
Oleg Sklyar |
Visualization of high-throughput assays in microtitre plate or
chamber slide format |
spotSegmentation
|
Chris Fraley |
Microarray Spot Segmentation and Gridding for Blocks of
Microarray Spots |
sscore
|
Richard Kennedy |
S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
ssize
|
Gregory R. Warnes |
Estimate Microarray Sample Size |
SSPA
|
Maarten van Iterson |
Sample Size and Power Analysis for Microarray Data |
stam
|
Claudio Lottaz |
Structured Analysis of Microarray Data |
stepNorm
|
Yuanyuan Xiao |
Stepwise normalization functions for cDNA microarrays |
TargetSearch
|
Alvaro Cuadros-Inostroza |
A package for the analysis of GC-MS metabolite profiling data. |
tilingArray
|
Zhenyu Xu |
Transcript mapping with high-density oligonucleotide tiling
arrays |
timecourse
|
Yu Chuan Tai |
Statistical Analysis for Developmental Microarray Time Course
Data |
tkWidgets
|
J. Zhang |
R based tk widgets |
topGO
|
Adrian Alexa |
topGO: Enrichment analysis for Gene Ontology |
tspair
|
Jeffrey T. Leek |
Top Scoring Pairs for Microarray Classification |
twilight
|
Stefanie Scheid |
Estimation of local false discovery rate |
TypeInfo
|
Duncan Temple Lang |
Optional Type Specification Prototype |
VanillaICE
|
Robert Scharpf |
A Hidden Markov Model for high throughput genotyping arrays |
vbmp
|
Nicola Lama |
Variational Bayesian Multinomial Probit Regression |
vsn
|
Wolfgang Huber |
Variance stabilization and calibration for microarray data |
weaver
|
Seth Falcon |
Tools and extensions for processing Sweave documents |
webbioc
|
Colin A. Smith |
Bioconductor Web Interface |
widgetTools
|
Jianhua Zhang |
Creates an interactive tcltk widget |
xcms
|
Colin A. Smith |
LC/MS and GC/MS Data Analysis |
XDE
|
Robert Scharpf |
XDE: a Bayesian hierarchical model for cross-study analysis of
differential gene expression |
xmapbridge
|
Tim Yates |
Export plotting files to the xmapBridge for visualisation in
X:Map |
xps
|
Christian Stratowa |
Processing and Analysis of Affymetrix Oligonucleotide Arrays
including Exon Arrays, Whole Genome Arrays and Plate Arrays |
yaqcaffy
|
Laurent Gatto |
Affymetrix expression data quality control and reproducibility
analysis |