• BicAT

  • Referenced in 16 articles [sw12371]
  • exploration of the gene expression data, e.g. microarrays...
  • PAGE

  • Referenced in 7 articles [sw23828]
  • Gene set enrichment analysis (GSEA) is a microarray data analysis method that uses predefined gene ... genes to identify significant biological changes in microarray data sets. GSEA is especially useful when ... gene expression changes in a given microarray data set is minimal or moderate. Results ... detect significantly changed gene sets from microarray data irrespective of different Affymetrix probe level analysis...
  • oligo

  • Referenced in 9 articles [sw06102]
  • NimbleGen arrays (XYS files). In most microarray technologies, a number of critical steps are required ... expressions is the most popular application of microarray technology. For this application, various groups have ... technology. Currently, other applications of microarrays are becoming more and more popular. We describe...
  • GEOquery

  • Referenced in 9 articles [sw17285]
  • Gene Expression Omnibus (GEO) and BioConductor. Microarray technology has become a standard molecular biology tool ... methods for the analysis of microarray and genomics data. We have developed a software tool ... tools. Facilitating analyses and meta-analyses of microarray data will increase the efficiency with which...
  • CLIFF

  • Referenced in 10 articles [sw35898]
  • CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts ... clustering biological samples using gene expression microarray data. This clustering problem is difficult for several...
  • uniCox

  • Referenced in 14 articles [sw19131]
  • Especially useful for high-dimensional data, including microarray data...
  • marrayClasses

  • Referenced in 7 articles [sw08346]
  • Exploratory Analysis and Normalization of cDNA Microarray Data. This chapter describes a collection of four ... analysis and normalization of two-color cDNA microarray fluorescence intensity data. R’s object-oriented ... systematic representation and manipulation of large microarray datasets of multiple types. The marrayClasses package contains ... automate data input and the creation of microarray-specific R objects for storing these data...
  • SVDMAN

  • Referenced in 8 articles [sw35896]
  • SVDMAN - singular value decomposition analysis of microarray data. .. Algorithms for the grouping method ... available in a software application called SVD Microarray ANalysis (SVDMAN). In addition to calculating ... SVDMAN provides a new means for using microarray data to develop hypotheses for gene associations...
  • TileMap

  • Referenced in 13 articles [sw35530]
  • Tiling array is a new type of microarray that can be used to survey genomic...
  • GOTM

  • Referenced in 9 articles [sw13869]
  • interesting genes using Gene Ontology hierarchies. Microarray and other high-throughput technologies are producing large ... sets of co-regulated genes identified from microarray analysis but is adaptable for use with...
  • HykGene

  • Referenced in 9 articles [sw23981]
  • selecting marker genes for phenotype classification using microarray gene expression data. MOTIVATION: Recent studies have ... shown that microarray gene expression data are useful for phenotype classification of many diseases...
  • fRMA

  • Referenced in 9 articles [sw34334]
  • Barcode. Preprocessing and analysis for single microarrays and microarray batches...
  • GeneNetWeaver

  • Referenced in 12 articles [sw22862]
  • inference methods. We are using in vivo microarray compendia side-by-side with synthetic...
  • Oncomine

  • Referenced in 7 articles [sw17289]
  • cancer gene expression profiles. DNA microarrays have been widely applied to cancer transcriptome analysis; however ... important analytic approaches have been applied to microarray analysis; however, their application is often limited ... deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types...
  • daMA

  • Referenced in 8 articles [sw06093]
  • efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial ... microarray data. Statistical details are described in Bretz et al. (2003, submitted...
  • Affymetrix

  • Referenced in 8 articles [sw14673]
  • Affymetrix GeneChip Operating Software (GCOS). Affymetrix® microarray solutions include all necessary components for a successful ... microarray experiment, from arrays and reagents to instruments and software. Our complete range of solutions...
  • CNV-seq

  • Referenced in 11 articles [sw17970]
  • commonly used for CNV detection, but the microarray platform has a number of inherent limitations...
  • CASPAR

  • Referenced in 6 articles [sw12242]
  • cancer from gene expression data. Motivation: DNA microarrays allow the simultaneous measurement of thousands ... times for the individual patient based on microarray measurements. CASPAR is based on a multivariate ... sample size settings, that are typical for microarray measurements. This enables CASPAR to automatically select...
  • minet

  • Referenced in 7 articles [sw08432]
  • from a dataset. Once fed with a microarray dataset, the package returns a network where ... tools for inferring transcriptional networks from microarray data. It is freely available from the Comprehensive...
  • GOstats

  • Referenced in 7 articles [sw11312]
  • GOstats. Tools for manipulating GO and microarrays. Bioconductor. A set of tools for interacting with ... microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple...