• sma

  • Referenced in 50 articles [sw36146]
  • package sma: Statistical Microarray Analysis. The package contains some simple functions for exploratory microarray analysis...
  • TM4

  • Referenced in 12 articles [sw26846]
  • system for microarray data management and analysis. Microarrays have emerged as the premier tool ... support of our ongoing work in microarray analysis of gene expression, we developed a suite ... manage, and analyze effectively data from DNA microarray experiments. The TM4 suite of tools consist ... Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment Viewer...
  • PAGE

  • Referenced in 7 articles [sw23828]
  • enrichment analysis (GSEA) is a microarray data analysis method that uses predefined gene sets ... different Affymetrix probe level analysis methods or different microarray platforms. Comparison of two aged muscle ... from microarray data irrespective of analysis methods or microarray platforms, and it was useful ... offer PAGE as a useful microarray analysis method...
  • impute

  • Referenced in 100 articles [sw14376]
  • estimation for DNA microarrays. Motivation: Gene expression microarray experiments can generate data sets with multiple ... values. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array ... estimation of missing values in gene microarray data. We implemented and evaluated three methods...
  • SVDMAN

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

  • Referenced in 16 articles [sw27064]
  • Using search engine technology for the analysis of microarray experiments. Background: Interpretation of simple microarray...
  • GOTM

  • Referenced in 9 articles [sw13869]
  • interesting genes using Gene Ontology hierarchies. Microarray and other high-throughput technologies are producing large ... created a web-based tool for data analysis and data visualization for sets of genes ... regulated genes identified from microarray analysis but is adaptable for use with other gene sets...
  • PROXIMUS

  • Referenced in 9 articles [sw04989]
  • areas, including association rule mining, DNA microarray analysis, and business analytics. The original release...
  • edgeR

  • Referenced in 48 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ... digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many ... genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves...
  • Oncomine

  • Referenced in 7 articles [sw17289]
  • expression profiles. DNA microarrays have been widely applied to cancer transcriptome analysis; however, the majority ... analytic approaches have been applied to microarray analysis; however, their application is often limited ... data to the biomedical research community. Our analysis has identified the genes, pathways, and networks ... deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types...
  • MAANOVA

  • Referenced in 4 articles [sw08357]
  • Software Package for the Analysis of Spotted cDNA Microarray Experiments ... describe a software package called MAANOVA (MicroArray ANalysis Of VAriance). MAANOVA is a collection ... experiments. MAANOVA provides specialized functions for microarray analysis in an open-ended format within flexible ... other functions for the rigorous statistical analysis of microarray data...
  • BicAT

  • Referenced in 16 articles [sw12371]
  • with the analysis and exploration of the gene expression data, e.g. microarrays...
  • GEOquery

  • Referenced in 9 articles [sw17285]
  • Gene Expression Omnibus (GEO) and BioConductor. Microarray technology has become a standard molecular biology tool ... Development core Team, 2005) for the analysis and comprehension of genomic data. The tools contained ... methods for the analysis of microarray and genomics data. We have developed a software tool...
  • daMA

  • Referenced in 8 articles [sw06093]
  • experiments and for the statistical analysis of factorial microarray data. Statistical details are described...
  • samr

  • Referenced in 3 articles [sw13903]
  • Significance analysis of microarrays – samr: R package. samr: SAM: Significance Analysis of Microarrays. Significance Analysis...
  • WebArrayDB

  • Referenced in 3 articles [sw37317]
  • WebArrayDB: cross-platform microarray data analysis ... public data repository. Motivation: Cross-platform microarray analysis is an increasingly important research tool ... storing, integrating and analyzing large amounts of microarray data obtained from different array platforms ... Results: An open source integrated microarray database and analysis suite, WebArrayDB (http://www.webarraydb.org), has been...
  • EDGE

  • Referenced in 9 articles [sw13105]
  • software program for the significance analysis of DNA microarray experiments. EDGE can perform both standard...
  • ArrayMining

  • Referenced in 2 articles [sw25183]
  • ArrayMining: A Modular Web-Application for Microarray Analysis Combining Ensemble and Consensus Methods with Cross ... single interface would simplify many microarray analysis tasks. RESULTS: We present ArrayMining.net, a web-application ... microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction ... free web-application for microarray analysis combining a broad choice of algorithms based on ensemble...
  • fRMA

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

  • Referenced in 4 articles [sw35496]
  • package lemma: Laplace approximated EM Microarray Analysis. LEMMA is used to detect ”nonnull genes” - genes ... average response in group 2, in normalized microarray data. LEMMA is an implementation...