Bioconductor Software Packages

Bioconductor version: 2.8

Package Maintainer Title
a4 Tobias Verbeke Automated Affymetrix Array Analysis Umbrella Package
a4Base Tobias Verbeke Automated Affymetrix Array Analysis Base Package
a4Classif Tobias Verbeke Automated Affymetrix Array Analysis Classification Package
a4Core Tobias Verbeke Automated Affymetrix Array Analysis Core Package
a4Preproc Tobias Verbeke Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting Tobias Verbeke Automated Affymetrix Array Analysis Reporting Package
ABarray Yongming Andrew Sun Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
aCGH Peter Dimitrov Classes and functions for Array Comparative Genomic Hybridization data.
ACME Sean Davis Algorithms for Calculating Microarray Enrichment (ACME)
ADaCGH2 Ramon Diaz-Uriarte Analysis of data from aCGH experiments using parallel computing and ff objects
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
affyILM Myriam Kroll and Fabrice Berger Linear Model of background subtraction and the Langmuir isotherm
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
AgiMicroRna Pedro Lopez-Romero Processing and Differential Expression Analysis of Agilent microRNA chips
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
AnnotationFuncs Stefan McKinnon Edwards Annotation translation functions
annotationTools Alexandre Kuhn Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
anota Ola Larsson ANalysis Of Translational Activity (ANOTA).
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
ArrayExpressHTS Angela Goncalves, Andrew Tikhonov ArrayExpress High Throughput Sequencing Processing Pipeline
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
attract Jessica Mar Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
BAC Raphael Gottardo Bayesian Analysis of Chip-chip experiment
BayesPeak Jonathan Cairns Bayesian Analysis of ChIP-seq Data
baySeq Thomas J. Hardcastle Empirical Bayesian analysis of patterns of differential expression in count data
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
BeadDataPackR Mike Smith Compression of Illumina BeadArray data
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
BHC Rich Savage Bayesian Hierarchical Clustering
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
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, COSMIC ,Wormbase and Gramene)
BioMVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes That Use Biobase
BioNet Marcus Dittrich Routines for the functional analysis of biological networks
BioSeqClass Li Hong Classification for Biological Sequences
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
BUS Yuanhua Liu Gene network reconstruction
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 Biocore Team c/o BioC user list Category Analysis
cellHTS Ligia Bras Analysis of cell-based screens
cellHTS2 Florian Hahne Analysis of cell-based screens - revised version of cellHTS
CGEN William Wheeler An R package for analysis of case-control studies in genetic epidemiology
CGHbase Sjoerd Vosse CGHbase: Base functions and classes for arrayCGH data analysis.
CGHcall Mark van de Wiel Calling aberrations for array CGH tumor profiles.
cghMCR J. Zhang Find chromosome regions showing common gains/losses
CGHnormaliter Bart P.P. van Houte Normalization of array CGH data with imbalanced aberrations.
CGHregions Sjoerd Vosse Dimension Reduction for Array CGH Data with Minimal Information Loss.
charm Martin Aryee Analysis of DNA methylation data from CHARM microarrays
ChemmineR ChemmineR Team Analysis of Small Molecule and Screening Data
ChIPpeakAnno Lihua Julie Zhu Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
chipseq Biocore Team c/o BioC user list chipseq: A package for analyzing chipseq data
ChIPseqR Peter Humburg Identifying Protein Binding Sites in High-Throughput Sequencing Data
ChIPsim Peter Humburg Simulation of ChIP-seq experiments
chopsticks Hin-Tak Leung The snp.matrix and X.snp.matrix classes
ChromHeatMap Tim F. Rayner Heat map plotting by genome coordinate
clippda Stephen Nyangoma A package for the clinical proteomic profiling data analysis
Clonality Irina Ostrovnaya Clonality testing
clst Noah Hoffman Classification by local similarity threshold
clstutils Noah Hoffman Tools for performing taxonomic assignment.
clusterProfiler Guangchuang Yu statistical analysis and visulization of functional profiles for genes and gene clusters
clusterStab James W. MacDonald Compute cluster stability scores for microarray data
CMA Christoph Bernau Synthesis of microarray-based classification
cn.farms Andreas Mitterecker, Djork-Arne Clevert cn.farms - Factor Analysis for copy number estimation
CNTools J. Zhang Convert segment data into a region by sample matrix to allow for other high level computational analyses.
CNVtools Chris Barnes A package to test genetic association with CNV data
CoCiteStats Biocore Team c/o BioC user list Different test statistics based on co-citation.
codelink Diego Diez Manipulation of Codelink Bioarrays data.
CoGAPS Elana J. Fertig, Michael F. Ochs Coordinated Gene Activity in Pattern Sets
ConsensusClusterPlus Matt Wilkerson ConsensusClusterPlus
convert Yee Hwa (Jean) Yang Convert Microarray Data Objects
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
coRNAi Elin Axelsson Analysis of co-knock-down RNAi data
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
CRImage Henrik Failmezger, Yinyin Yuan CRImage a package to classify cells and calculate tumour cellularity
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.
CSAR Jose M Muino Statistical tools for the analysis of ChIP-seq data
ctc Antoine Lucas Cluster and Tree Conversion.
cycle Matthias Futschik Significance of periodic expression pattern in time-series data
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
ddCt Jitao David Zhang The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
DEDS Yuanyuan Xiao Differential Expression via Distance Summary for Microarray Data
DEGraph Laurent Jacob Two-sample tests on a graph
DEGseq Likun Wang Identify Differentially Expressed Genes from RNA-seq data
DESeq Simon Anders Digital gene expresion analysis based on the negative binomial distribution
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 The GASSCO method for correcting for slide-dependent 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 Gautier Meta-data and tools for E. coli
edd Vince Carey expression density diagnostics
edgeR Mark Robinson, Davis McCarthy, Gordon Smyth Empirical analysis of digital gene expression data in R
eisa Gabor Csardi Expression data analysis via the Iterative Signature Algorithm
ENVISIONQuery Alex Lisovich, Roger Day Retrieval from the ENVISION bioinformatics data portal into R
ExiMiR Sylvain Gubian R functions for the normalization of Exiqon miRNA array data
explorase Michael Lawrence GUI for exploratory data analysis of systems biology data
ExpressionView Gabor Csardi Visualize biclusters identified in gene expression data
externalVector Biocore Team c/o BioC user list Vector objects for R with external storage
fabia Sepp Hochreiter FABIA: Factor Analysis for Bicluster Acquisition
factDesign Denise Scholtens Factorial designed microarray experiment analysis
farms Djork-Arne Clevert FARMS - Factor Analysis for Robust Microarray Summarization
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.
flowFP Herb Holyst Fingerprinting for Flow Cytometry
flowMeans Nima Aghaeepour Non-parametric Flow Cytometry Data Gating
flowMerge Greg Finak Cluster Merging for Flow Cytometry Data
flowPhyto David M. Schruth Methods for Continuous Flow Cytometry
flowPlots N. Hawkins flowPlots: analysis plots and data class for gated flow cytometry data
flowQ F. Hahne Quality control for flow cytometry
flowStats Florian Hahne and Chao-Jen Wong Statistical methods for the analysis of flow cytometry data
flowTrans Greg Finak Parameter Optimization for Flow Cytometry Data Transformation
flowUtils Nishant Gopalakrishnan Utilities for flow cytometry
flowViz Florian Hahne Visualization for flow cytometry
frma Matthew N. McCall Frozen RMA and Barcode
frmaTools Matthew N. McCall Frozen RMA Tools
gaga David Rossell GaGa hierarchical model for microarray data analysis
gage Weijun Luo Generally Applicable Gene-set Enrichment for Pathway Analysis
gaggle Christopher Bare Broadcast data between R and Gaggle
gaia S. Morganella GAIA: An R package for genomic analysis of significant chromosomal aberrations.
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
GeneAnswers Gang Feng, Pan Du and Tian Xia Integrated Interpretation of Genes
genefilter Biocore Team c/o BioC user list genefilter: methods for filtering genes from microarray experiments
genefu Benjamin Haibe-Kains, Markus Schroeder Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.
GeneGA Zhenpeng Li Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
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 Stability and Aggregation of ranked gene lists
GeneSpring Thon de Boer GeneSpring R Integration Functions
GeneticsDesign The R Genetics Project Functions for designing genetics studies
GeneticsPed David Henderson Pedigree and genetic relationship functions
GeneTraffic Daniel Iordan GeneTraffic R Integration Functions
genoCN Wei Sun genotyping and copy number study tools
GenomeGraphs Steffen Durinck Plotting genomic information from Ensembl
genomeIntervals Julien Gagneur Operations on genomic intervals
genomes Chris Stubben Genome sequencing project metadata
GenomicFeatures Biocore Team c/o BioC user list Tools for making and manipulating transcript centric annotations
GenomicRanges Biocore Team c/o BioC user list Representation and manipulation of genomic intervals
Genominator James Bullard Analyze, manage and store genomic data
genoset Peter M. Haverty Provides classes similar to ExpressionSet for copy number analysis
GEOmetadb Jack Zhu A compilation of metadata from NCBI GEO
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
GEOsubmission Alexandre Kuhn Prepares microarray data for submission to GEO
GGBase Vince Carey infrastructure for genetics of gene expression (c) 2008 VJ Carey
GGtools Vince Carey software and data for genetics of gene expression (c) 2006 VJ Carey
girafe J. Toedling Genome Intervals and Read Alignments for Functional Exploration
GLAD Philippe Hupe Gain and Loss Analysis of DNA
GlobalAncova Manuela Hummel Calculates a global test for differential gene expression between groups
globaltest Jelle Goeman Testing groups of covariates/features for association with a response variable, with applications to gene set testing
goProfiles Alex Sanchez goProfiles: an R package for the statistical analysis of functional profiles
GOSemSim Guangchuang Yu GO-terms Semantic Similarity Measures
goseq Matthew Young Gene Ontology analyser for RNA-seq and other length biased data
GOstats Biocore Team c/o BioC user list 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 Seth Falcon 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
GSRI Julian Gehring Gene Set Regulation Index
GSVA Justin Guinney Gene Set Variation 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)
HTqPCR Heidi Dvinge Automated analysis of high-throughput qPCR data
HTSanalyzeR Xin Wang Gene set over-representation, enrichment and network analyses for high-throughput screens
hyperdraw Paul Murrell Visualizing Hypergaphs
hypergraph Biocore Team c/o BioC user list A package providing hypergraph data structures
ibh Kircicegi Korkmaz Interaction Based Homogeneity for Evaluating Gene Lists
Icens Biocore Team c/o BioC user list NPMLE for Censored and Truncated Data
iChip Qianxing Mo Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
idiogram Karl J. Dykema idiogram
iFlow Kyongryun Lee GUI based visualization for flow cytometry
imageHTS Gregoire Pau Analysis of high-throughput microscopy-based screens
impute Balasubramanian Narasimhan impute: Imputation for microarray data
inveRsion Alejandro Caceres Inversions in genotype data
IPPD Martin Slawski Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
IRanges Biocore Team c/o BioC user list Infrastructure for manipulating intervals on sequences
iSeq Qianxing Mo Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
IsoGeneGUI Setia Pramana A graphical user interface to conduct a dose-response analysis of microarray data
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
joda Ewa Szczurek JODA algorithm for quantifying gene deregulation using knowledge
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
keggorthology VJ Carey graph support for KO, KEGG Orthology
KEGGSOAP Biocore Team c/o BioC user list Client-side SOAP access KEGG
lapmix Yann Ruffieux Laplace Mixture Model in Microarray Experiments
LBE Cyril Dalmasso Estimation of the false discovery rate.
les Julian Gehring Identifying Differential Effects in Tiling Microarray Data
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Keith Satterley GUI for limma package
LiquidAssociation Yen-Yi Ho LiquidAssociation
LMGene Blythe Durbin-Johnson LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
logicFS Holger Schwender Identification of SNP Interactions
logitT Tobias Guennel logit-t Package
lol Yinyin Yuan Lots Of Lasso
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 Methylation and Expression Microarrays
LVSmiRNA Stefano Calza LVS normalization for Agilent miRNA data
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 Maria Jose Nueda Significant Gene Expression Profile Differences in Time Course Microarray Data
MassArray Reid F. Thompson Analytical Tools for MassArray Data
MassSpecWavelet Pan Du Mass spectrum processing by wavelet-based algorithms
MBCB Jeff Allen MBCB (Model-based Background Correction for Beadarray)
mBPCR P.M.V. Rancoita Bayesian Piecewise Constant Regression for DNA copy number estimation
mcaGUI Wade K. Copeland Microbial Community Analysis GUI
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
MEDIPS Lukas Chavez MeDIP-Seq data analysis
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
methVisual Arie Zackay Methods for visualization and statistics on DNA methylation data
methylumi Sean Davis Handle Illumina methylation data
Mfuzz Matthias Futschik Soft clustering of time series gene expression data
mgsa Sebastian Bauer Model-based gene set analysis
MiChip Jonathon Blake MiChip Parsing and Summarizing Functions
microRNA Chao-Jen Wong Data and functions for dealing with microRNAs
minet Patrick E. Meyer Mutual Information NETworks
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
MLP Tobias Verbeke MLP
mosaics Dongjun Chung MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MotIV Eloi Mercier, Raphael Gottardo Motif Identification and Validation
MSnbase Laurent Gatto MSnbase: Base Functions and Classes for MS-based Proteomics
Mulcom Claudio Isella Calculates Mulcom test
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
NCIgraph Laurent Jacob Pathways from the NCI Pathways Database
nem Holger Froehlich Nested Effects Models to reconstruct phenotypic hierarchies
netresponse Leo Lahti NetResponse: functional network analysis
nnNorm Adi Laurentiu Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
NTW Yuanhua Liu Predict gene network using an Ordinary Differential Equation (ODE) based method
nudge N. Dean Normal Uniform Differential Gene Expression detection
NuPoP Ji-Ping Wang An R package for nucleosome positioning prediction
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 Preprocessing tools for oligonucleotide arrays.
oligoClasses Benilton Carvalho and Robert Scharpf Classes for high-throughput arrays supported by oligo and crlmm
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. Next Generation Sequencing secondary analysis for ncRNA quantification is also available.
ontoCAT Natalja Kurbatova Ontology traversal and search
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
OTUbase Daniel Beck Provides structure and functions for the analysis of OTU data
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
PatientGeneSets Simina M. Boca Patient-oriented gene-set analysis
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
phenoDist Xian Zhang Phenotypic distance measures
phenoTest Evarist Planet Tools to test correlation between gene expression and phenotype.
pickgene Brian S. Yandell Adaptive Gene Picking for Microarray Expression Data Analysis
PICS Arnaud Droit, Xuekui Zhang, Raphael Gottardo Probabilistic inference of ChIP-seq
pint Olli-Pekka Huovilainen Pairwise INTegration of functional genomics data
pkgDepTools Seth Falcon Package Dependency Tools
plateCore Errol Strain Statistical tools and data structures for plate-based flow cytometry
plgem Norman Pavelka Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
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
procoil Ulrich Bodenhofer Prediction of Oligomerization of Coiled Coil Proteins
PROMISE Xueyuan Cao PRojection Onto the Most Interesting Statistical Evidence
puma Richard Pearson, Li Zhang Propagating Uncertainty in Microarray Analysis
pvac Jun Lu, Pierre R. Bushel PCA-based gene filtering for Affymetrix arrays
qpcrNorm Jessica Mar Data-driven normalization strategies for high-throughput qPCR data.
qpgraph Robert Castelo Reverse engineering of molecular regulatory networks with qp-graphs
qrqc Vince Buffalo Quick Read Quality Control
quantsmooth Jan Oosting Quantile smoothing and genomic visualization of array data
qvalue John D. Storey Q-value estimation for false discovery rate control
R453Plus1Toolbox Hans-Ulrich Klein A package for importing and analyzing data from Roche's Genome Sequencer System.
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
RCytoscape Paul Shannon Display and manipulate graphs in Cytoscape
Rdbi Jianhua Zhang Generic database methods
RdbiPgSQL Jianhua Zhang PostgreSQL access
Rdisop Steffen Neumann Decomposition of Isotopic Patterns
RDRToolbox Christoph Bartenhagen A package for nonlinear dimension reduction with Isomap and LLE.
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
rGADEM Arnaud Droit de novo motif discovery
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
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
RMAPPER Heike Sichtig, Alberto Riva R interface to the MAPPER database of transcription factor binding sites
rMAT Arnaud Droit and Raphael Gottardo R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
RmiR Francesco Favero Package to work with miRNAs and miRNA targets with R
RNAinteract Bernd Fischer Estimate Pairwise Interactions from multidimensional features
RNAither Nora Rieber Statistical analysis of high-throughput RNAi screens
rnaSeqMap Michal Okoniewski rnaSeq analyses using xmapcore database
ROC Vince Carey utilities for ROC, with uarray focus
Rolexa Jacques Rougemont Statistical analysis of Solexa sequencing data
RPA Leo Lahti RPA: probe reliability and differential gene expression analysis
RpsiXML Jitao David Zhang R interface to PSI-MI 2.5 files
Rredland VJ Carey interface to redland RDF utilities
Rsamtools Biocore Team c/o BioC user list Import aligned BAM file format sequences into R / Bioconductor
rsbml Michael Lawrence R support for SBML, using libsbml
Rsubread Wei Shi Rsubread: a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads
RTCA Jitao David Zhang Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche
RTools4TB Aurelie Bergon Data mining of public microarray data through connections to the TranscriptomeBrowser database.
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
SamSPECTRAL Habil Zare Identifies cell population in flow cytometry data.
SBMLR Tomas Radivoyevitch SBML-R Interface and Analysis Tools
ScISI Tony Chiang In Silico Interactome
segmentSeq Thomas J. Hardcastle Methods for identifying small RNA loci from high-throughput sequencing data
seqbias Daniel Jones Estimation of per-position bias in high-throughput sequencing data
seqLogo Oliver Bembom Sequence logos for DNA sequence alignments
ShortRead Biocore Team c/o BioC user list 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 on two human genomic datasets
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
SJava Martin Morgan The Omegahat interface for R and Java.
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.
snm Brig Mecham Supervised Normalization of Microarrays
SNPchip Robert Scharpf Classes and Methods for high throughput SNP chip data
snpMatrix David Clayton The snp.matrix and X.snp.matrix classes
snpStats David Clayton SnpMatrix and XSnpMatrix classes and methods
SpeCond Florence Cavalli Condition specific detection from expression data
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 Wolfgang Huber Visualization of high-throughput assays in microtitre plate or slide format
spotSegmentation Chris Fraley Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
SQUADD Martial Sankar Add-on of the SQUAD Software
SRAdb Jack Zhu A compilation of metadata from NCBI SRA and tools
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
Starr Benedikt Zacher Simple tiling array analysis of Affymetrix ChIP-chip data
stepNorm Yuanyuan Xiao Stepwise normalization functions for cDNA microarrays
survcomp Benjamin Haibe-Kains, Markus Schroeder Performance Assessment and Comparison for Survival Analysis
TargetSearch Alvaro Cuadros-Inostroza A package for the analysis of GC-MS metabolite profiling data.
TDARACNE Zoppoli Pietro Network reverse engineering from time course data.
TEQC Manuela Hummel Quality control for target capture experiments
tigre Antti Honkela Transcription factor Inference through Gaussian process Reconstruction of Expression
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
TurboNorm Maarten van Iterson A fast scatterplot smoother suitable for microarray normalization
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
Vega Sandro Morganella An R package for copy number data segmentation
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 Ralf Tautenhahn 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
xmapcore Tim Yates Core access to the xmap database (installed separately)
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

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