Bioconductor version: 2.5
Package | Maintainer | Title |
---|---|---|
ABarray | Yongming Andrew Sun |
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (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) |
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 |
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 |
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 |
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 |
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 |
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 | Yin Jin |
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 | 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 | 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 | Mark van de Wiel |
Dimension Reduction for Array CGH Data with Minimal Information Loss. |
ChemmineR | Y. Eddie Cao |
A Compound Data Mining Framework |
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 |
ChIPsim | Peter Humburg |
Simulation of ChIP-seq experiments |
ChromHeatMap | Tim F. Rayner |
Heat map plotting by genome coordinate |
clippda | Stephen Nyangoma |
A package for the clinical proteomic profiling data analysis |
clusterStab | James W. MacDonald |
Compute cluster stability scores for microarray data |
CMA | Christoph Bernau |
Synthesis of microarray-based classification |
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 | 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 |
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. |
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 |
DEDS | Yuanyuan Xiao |
Differential Expression via Distance Summary for Microarray Data |
DEGseq | Likun Wang |
Identify Differentially Expressed Genes from RNA-seq 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 |
The GASSCO method, for correcting for slide-depedent gene-specific dye bias |
DynDoc | Biocore Team c/o BioC user list
|
Dynamic document tools |
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 |
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. |
flowFP | Herb Holyst |
Fingerprinting for Flow Cytometry |
flowMerge | Greg Finak |
Cluster Merging for Flow Cytometry Data |
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 |
GeneAnswers | Gang Feng |
Integrated Interpretation of Genes |
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 |
Stability and Aggregation of ranked gene lists |
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 |
GenomicFeatures | Biocore Team c/o BioC user list
|
Support package for genomic annotations |
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 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 |
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 | 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 |
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 |
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 qPCR data |
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 |
LiquidAssociation | Yen-Yi Ho |
LiquidAssociation |
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 |
mBPCR | P.M.V. Rancoita |
Bayesian Piecewise Constant Regression for DNA copy number estimation |
MCRestimate | Marc Johannes |
Misclassification error estimation with cross-validation |
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 |
methylumi | Sean Davis |
Handle Illumina methylation data |
Mfuzz | Matthias Futschik |
Soft clustering of time series gene expression data |
MiChip | Jonathon Blake |
MiChip Parsing and Summarizing Functions |
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 arrays supported by oligo |
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 |
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 |
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) |
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 |
RBGL | Li Long |
An interface to the BOOST graph library |
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 |
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 |
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 |
RNAither | Nora Rieber |
Statistical analysis of high-throughput RNAi screens |
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 |
rsbml | Michael Lawrence |
R support for SBML, using libsbml |
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 |
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 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 |
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 |
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 |
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 |
Starr | Benedikt Zacher |
Simple tiling array analysis of Affymetrix ChIP-chip 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 |
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