• Bioconductor

  • Referenced in 320 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses ... software packages, and an active user community. Bioconductor is also available as an Amazon Machine...
  • edgeR

  • Referenced in 53 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ... different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression...
  • affy

  • Referenced in 39 articles [sw08345]
  • Public License. It is part of the Bioconductor project and can be obtained from...
  • vsn

  • Referenced in 29 articles [sw06105]
  • Variance stabilization and calibration for microarray data Bioconductor version: Release (2.10) The package implements...
  • flowClust

  • Referenced in 25 articles [sw14266]
  • flowClust Bioconductor package: Robust model-based clustering using a t-mixture model with...
  • BGX

  • Referenced in 15 articles [sw06935]
  • Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips. BGX is a new Bioconductor...
  • GEOquery

  • Referenced in 10 articles [sw17285]
  • between the Gene Expression Omnibus (GEO) and BioConductor. Microarray technology has become a standard molecular ... nearly 140 000 gene expression experiments. The BioConductor project (Gentleman ... genomic data. The tools contained in the BioConductor project represent many state ... wealth of information within GEO directly from BioConductor, eliminating many the formatting and parsing problems...
  • graph

  • Referenced in 16 articles [sw08267]
  • package to handle graph data structures. Bioconductor version: Release (2.13). A package that implements some...
  • TWILIGHT

  • Referenced in 9 articles [sw06788]
  • genes. Our algorithm is implemented in the Bioconductor compatible R package TWILIGHT version 1.0.1, which ... from http://compdiag.molgen.mpg.de/software or from the Bioconductor project at http://www.bioconductor.org...
  • Ebimage

  • Referenced in 12 articles [sw18998]
  • LGPL license and available from the Bioconductor project (http://www.bioconductor.org/packages/release/bioc/html/EBImage.html)....
  • KEGGgraph

  • Referenced in 8 articles [sw06934]
  • approach to KEGG PATHWAY in R and bioconductor. Motivation: KEGG PATHWAY is a service ... software package KEGGgraph in R and Bioconductor, an interface between KEGG pathways and graph models...
  • BayesPeak

  • Referenced in 8 articles [sw18843]
  • BayesPeak algorithm and is compatible with downstream BioConductor packages. The BayesPeak package introduces ... peak-callers. Availability: Available as part of BioConductor version 2.6. URL: http://bioconductor.org/packages/release/bioc/html/BayesPeak.html...
  • maSigPro

  • Referenced in 11 articles [sw11024]
  • freely available from the Bioconductor contributed packages repository and from http://www.ivia.es/centrogenomica/bioinformatics.htm...
  • Affycomp III

  • Referenced in 11 articles [sw14610]
  • graphics toolbox as part of the Bioconductor project (http://www.bioconductor.org), a webtool is available...
  • marrayClasses

  • Referenced in 7 articles [sw08346]
  • Bioconductor R Packages for Exploratory Analysis and Normalization of cDNA Microarray Data. This chapter describes ... packages were developed as part of the Bioconductor project, which aims more generally to produce...
  • oligo

  • Referenced in 9 articles [sw06102]
  • implemented in the package oligo available from Bioconductor...
  • ShortRead

  • Referenced in 6 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...
  • daMA

  • Referenced in 8 articles [sw06093]
  • Bioconductor version: Release (2.10) This package contains functions for the efficient design of factorial...
  • minet

  • Referenced in 8 articles [sw08432]
  • Network (CRAN) as well as from the Bioconductor website...
  • GOstats

  • Referenced in 8 articles [sw11312]
  • GOstats. Tools for manipulating GO and microarrays. Bioconductor. A set of tools for interacting with...