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  • minet
  • Referenced in 7 articles [sw08432]
  • Network (CRAN) as well as from the Bioconductor website...

  • GOstats
  • Referenced in 7 articles [sw11312]
  • GOstats. Tools for manipulating GO and microarrays. Bioconductor. A set of tools for interacting with...

  • snpStats
  • Referenced in 7 articles [sw11396]
  • snpStats: SnpMatrix and XSnpMatrix classes and methods. Bioconductor. Classes and statistical methods for large...

  • ROAST
  • Referenced in 7 articles [sw17318]
  • implemented as a function in the Bioconductor package limma available from www.bioconductor.org...

  • MEIGO
  • Referenced in 6 articles [sw08492]
  • package has been submitted to Bioconductor. We evaluate MEIGO against optimization benchmarks, and illustrate...

  • VanillaICE
  • Referenced in 6 articles [sw11310]
  • Markov Model for high throughput genotyping arrays. Bioconductor. Hidden Markov Models for characterizing chromosomal alterations...

  • CGHcall
  • Referenced in 6 articles [sw17968]
  • Bioconductor package CGHcall. Calling aberrations for array CGH tumor profiles. Calls aberrations for array...

  • Minfi
  • Referenced in 6 articles [sw23478]
  • Minfi: a flexible and comprehensive bioconductor package for the analysis of infinium DNA methylation microarrays...

  • ShortRead
  • Referenced in 4 articles [sw16605]
  • ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data ... ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities...

  • GEOmetadb
  • Referenced in 3 articles [sw17290]
  • available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export ... databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project...

  • CMA
  • Referenced in 3 articles [sw17863]
  • comprehensive Bioconductor package for supervised classification with high dimensional data. Background: For the last eight ... this article, we introduce a new Bioconductor package called CMA (standing for ”C lassification ... approaches. It is freely available from the Bioconductor website at http://bioconductor.org/packages/2.3/bioc/html/CMA.html....

  • BioNet
  • Referenced in 5 articles [sw13828]
  • integrated network analysis using R and BioConductor. It includes the statistics for the integration...

  • Knorm
  • Referenced in 5 articles [sw16562]
  • Knorm) that is freely available from the Bioconductor website...

  • Simpleaffy
  • Referenced in 3 articles [sw06937]
  • Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Quality Control ... successful microarray data analysis. Simpleaffy is a BioConductor package that provides access to a variety...

  • lumi
  • Referenced in 3 articles [sw08431]
  • designed for Affymetrix microarrays. lumi is a Bioconductor package especially designed to process the Illumina ... results can be easily integrated with other Bioconductor packages to construct a statistical data analysis...

  • csaw
  • Referenced in 3 articles [sw17944]
  • csaw: A bioconductor package for differential binding analysis of ChIP-seq data using sliding windows ... freely available from the open-source Bioconductor project...

  • CARMAweb
  • Referenced in 3 articles [sw36164]
  • CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. CARMAweb allows ... using functions provided by the BioConductor packages. The web application bases on the Java...

  • gaga
  • Referenced in 4 articles [sw06101]
  • flexible model for differential expression analysis Bioconductor version: Release (2.10) Implements the GaGa model...

  • Puma
  • Referenced in 4 articles [sw19121]
  • Puma: a bioconductor package for propagating uncertainty in microarray analysis. Most analyses of Affymetrix GeneChip...

  • arrayQualityMetrics
  • Referenced in 2 articles [sw11307]
  • arrayQualityMetrics–a bioconductor package for quality assessment of microarray data. This package generates microarray quality ... metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch...