BioConductor Packages - 1.6 Release

 Package   Version   Title 
  aCGH   1.1.7   Classes and functions for Array Comparative Genomic Hybridization data. 
  affy   1.6.7   Methods for Affymetrix Oligonucleotide Arrays 
  affycomp   1.4.3   Graphics Toolbox for Assessment of Affymetrix Expression Measures 
  affydata   1.4.1   Affymetrix Data for Demonstration Purpose 
  affylmGUI   1.2.7   GUI for affy analysis using limma package 
  affypdnn   1.1.0   Probe Dependent Nearest Neighbours (PDNN) for the affy package 
  affyPLM   1.3.3   Methods for fitting probe-level models 
  altcdfenvs   1.1.11   alternative cdfenvs 
  annaffy   1.0.18   Annotation tools for Affymetrix biological metadata 
  AnnBuilder   1.5.31   Bioconductor annotation data package builder 
  annotate   1.5.16   Annotation for microarrays 
  apComplex   1.1.5   Estimate protein complex membership using AP-MS protein data 
  arrayMagic   1.5.8   two-colour cDNA array quality control and preprocessing 
  arrayQuality   1.0.11   Assessing array quality on spotted arrays 
  bim   1.0.3   Bayesian Interval Mapping Diagnostics 
  Biobase   1.5.12   Biobase: Base functions for Bioconductor 
  bioDist   1.0.0   Different distance measures 
  biomaRt   1.0.4   Interface to BioMart databases (e.g. Ensembl) 
  Biostrings   1.1.1   String objects reepresenting biological sequences 
  bridge   1.0.1   Bayesian Robust Inference for Differential Gene Expression 
  Category   1.0.1   Category Analysis 
  ChromoViz   1.0   Multimodal visualization of gene expression 
  CoCiteStats   1.0.0   Different test statistics based on co-citation. 
  convert   1.1.11   Convert Microarray Data Objects 
  ctc   1.2.7   Cluster and Tree Conversion. 
  daMA   1.0.1   Efficient design and analysis of factorial two-colour microarray data 
  DEDS   1.0.5   Differential Expression via Distance Summary for Microarray Data 
  DNAcopy   1.1.2   DNA copy number data analysis 
  DynDoc   1.5.5   Dynamic document tools 
  EBarrays   1.0.19   Empirical Bayes for Microarrays 
  ecolitk   1.0.1   Meta-data and tools for E. coli 
  edd   1.5.1   expression density diagnostics 
  factDesign   1.1.5   Factorial designed microarray experiment analysis 
  gcrma   1.1.4   Background Adjustment Using Sequence Information 
  genArise   1.3.2   Microarray Analysis tool 
  genefilter   1.6.3   genefilter: filter genes 
  GeneMeta   1.0.0   MetaAnalysis for High Throughput Experiments 
  geneplotter   1.6.1   Grapics related functions for Bioconductor 
  geneRecommender   1.0.2   A gene recommender algorithm to identify genes coexpressed with a query set of genes 
  GeneSpring   2.0.0   GeneSpring R Integration Functions 
  GeneTraffic   1.0.6   GeneTraffic R Integration Functions 
  GeneTS   2.4.1   Microarray Time Series and Network Analysis 
  gff3Plotter   1.0.2   Structuring and Plotting GFF3 Data Files 
  GLAD   1.0.4   Gain and Loss Analysis of DNA 
  globaltest   3.0.5   Testing Association of a Group of Genes with a Clinical Variable 
  goCluster   1.0.3   Analysis of clustering results in conjunction with annotation data. 
  GOstats   1.1.3   Tools for manipulating GO and microarrays. 
  goTools   1.0.6   Functions for Gene Ontology database 
  gpls   1.0.6   Classification using generalized partial least squares 
  graph   1.5.9   graph: A package to handle graph data structures 
  GraphAT   1.0.0   Graph Theoretic Association Tests 
  hexbin   1.2.7   Hexagonal Binning Routines 
  hopach   1.1.1   Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) 
  hypergraph   1.0.0   A package providing hypergraph data structures 
  Icens   1.0.0   NPMLE for Censored and Truncated Data 
  ideogram   1.0.1   ideogram 
  impute   1.0.2   impute: Imputation for microarray data 
  iSPlot   1.0.8   Linking Plots 
  KEGGSOAP   1.1.5   Client-side SOAP access KEGG 
  limma   1.9.6   Linear Models for Microarray Data 
  limmaGUI   1.3.9   GUI for limma package 
  LPE   1.1.5   Methods for analyzing microarray data using Local Pooled Error (LPE) method 
  macat   1.2.0   MicroArray Chromosome Analysis Tool 
  maDB   1.0.1   Micro array database and utility functions for micro array analysis. 
  made4   1.0.0   Multivariate analysis of microarray data using ADE4 
  makecdfenv   1.5.2   CDF Environment Maker 
  marray   1.6.3   Exploratory analysis for two-color spotted microarray data 
  matchprobes   1.0.22   Tools for sequence matching of probes on arrays 
  MCRestimate   1.2.6   Misclassification error estimation with cross-validation 
  MeasurementError.cor   1.0.2   Measurement Error model estimate for correlation coefficient 
  MergeMaid   2.0.1   Merge Maid 
  MiPP   1.0.2   MiPP (Misclassification Penalized Posterior)-based Classification 
  MLInterfaces   1.0.10   MLInterfaces 
  msbase   1.1.1   Basic classes and methods for mass spectrometric mass list manipulation. 
  mscalib   1.0.2   Calibration and filtering of mass spectrometric peak(mass) lists. 
  multtest   1.6.0   Resampling-based multiple hypothesis testing 
  nnNorm   1.1.0   Spatial and intensity based normalization of cDNA microarray data based on robust neural nets 
  OLIN   1.3.3   Optimized local intensity-dependent normalisation of two-color microarrays 
  OLINgui   1.0.1   Graphical user interface for OLIN 
  ontoTools   1.4.8   graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management 
  pairseqsim   1.0.4   pairwise sequence alignment similarity simple. 
  pamr   1.22   Pam: prediction analysis for microarrays 
  pgUtils   1.0.3   Utility functions for PostgreSQL databases 
  pickgene   1.0.0   Adaptive Gene Picking for Microarray Expression Data Analysis 
  plgem   1.0.0   Power Law Global Error Model 
  plier   1.0.0   Implements the Affymetrix PLIER algorithm 
  prada   1.3.1   Data analysis for cell-based functional assays 
  PROcess   1.3.4   Ciphergen SELDI-TOF Processing 
  qvalue   1.1.0   Q-value estimation for false discovery rate control 
  rama   1.0.1   Robust Analysis of MicroArrays 
  RankProd   1.0.0   Rank Product method for identifying differentially expressed genes. 
  RBGL   1.3.13   Test interface to boost C++ graph lib 
  Rdbi   1.1.2   Generic database methods 
  RdbiPgSQL   1.1.4   PostgreSQL access 
  reposTools   1.5.19   Repository tools for R 
  Resourcerer   1.1.2   Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. 
  rfcdmin   1.0.0   Minimal Data Library for RFlowCyt examples 
  rflowcyt   1.0.1   Statistical tools and data structures for analytic flow cytometry 
  Rgraphviz   1.5.10   Provides plotting capabilities for R graph objects 
  rhdf5   1.4.1   An HDF5 interface for R 
  ROC   1.1.1   utilities for ROC, with uarray focus 
  RSNPper   1.0.5   interface to chip.org::SNPper for SNP-related data 
  Ruuid   1.5.3   Ruuid: Provides Universally Unique ID values 
  safe   1.0.0   Significance Analysis of Function and Expression 
  SAGElyzer   1.5.2   A package that deals with SAGE libraries 
  sagenhaft   1.0.0   Collection of functions for reading and comparing SAGE libraries 
  siggenes   1.2.17   SAM and Efron's empirical Bayes approaches 
  simpleaffy   2.0.16   Very simple high level analysis of Affymetrix data 
  SNAData   1.1.1   Social Networks Analysis Data Examples 
  splicegear   1.0.10   splicegear 
  spotSegmentation   1.1.1   Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots 
  ssize   1.0.1   Estimate Microarry Sample Size 
  stam   1.0.9   Structured Analysis of Microarray Data 
  stepNorm   1.0.2   Stepwise normalization functions for cDNA microarrays 
  tilingArray   1.0.2   Analysis of tiling arrays 
  tkWidgets   1.5.23   R based tk widgets 
  twilight   1.1.0   Estimation of local false discovery rate 
  vsn   1.6.3   Variance stabilization and calibration for microarray data 
  webbioc   1.0.1   Bioconductor Web Interface 
  widgetInvoke   1.0.0   Evaluation widgets for functions 
  widgetTools   1.4.7   Creates an interactive tcltk widget 
  xcms   1.0.0   LC/MS and GC/MS Data Analysis