• impute

  • Referenced in 91 articles [sw14376]
  • Missing value estimation for DNA microarrays. Motivation: Gene expression microarray experiments can generate data sets ... estimation of missing values in gene microarray data. We implemented and evaluated three methods ... tools for accurate estimation of missing microarray data under a variety of conditions. Availability...
  • ARACNE

  • Referenced in 31 articles [sw17200]
  • present ARACNE, a novel algorithm, using microarray expression profiles, specifically designed to scale ... both a realistic synthetic dataset and a microarray dataset from human B cells. On synthetic ... approach should enhance our ability to use microarray data to elucidate functional mechanisms that underlie...
  • limma

  • Referenced in 48 articles [sw10458]
  • limma: Linear Models for Microarray Data. A survey is given of differential expression analyses using...
  • vsn

  • Referenced in 28 articles [sw06105]
  • Variance stabilization and calibration for microarray data Bioconductor version: Release (2.10) The package implements ... method for normalising microarray intensities, both between colours within array, and between arrays. The method ... likelihood estimator for the stochastic model of microarray data described in the references (see vignette...
  • edgeR

  • Referenced in 44 articles [sw06936]
  • digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many...
  • GSA

  • Referenced in 37 articles [sw18747]
  • differentially expressed groups of genes from a microarray experiment. The groups of genes are externally...
  • EBarrays

  • Referenced in 31 articles [sw08355]
  • Parametric Empirical Bayes Methods for Microarrays. We have developed an empirical Bayes methodology for gene...
  • SAM

  • Referenced in 20 articles [sw08356]
  • Detecting Differential Gene Expression in DNA Microarrays. SAM is a computer package for correlating gene ... detecting differential gene expression in DNA microarrays. Some recently developed methodology for estimating false discovery...
  • GeneRank

  • Referenced in 16 articles [sw27064]
  • search engine technology for the analysis of microarray experiments. Background: Interpretation of simple microarray experiments ... algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about...
  • SparseLOGREG

  • Referenced in 25 articles [sw11449]
  • context of cancer diagnosis using microarray data. Results: The gene selection method suggested in this...
  • penalized

  • Referenced in 24 articles [sw06071]
  • performance, it will be applied to several microarray data sets. An R package penalized, which...
  • TM4

  • Referenced in 11 articles [sw26846]
  • free, open-source system for microarray data management and analysis. Microarrays have emerged ... 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 ... four major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS...
  • multtest

  • Referenced in 20 articles [sw08262]
  • identifying differentially expressed genes in DNA microarray experiments...
  • GOstat

  • Referenced in 18 articles [sw10975]
  • Modern experimental techniques, as for example DNA microarrays, as a result usually produce a long...
  • FatiGO

  • Referenced in 18 articles [sw12318]
  • context of a genome-scale experiment (DNA microarray, proteomics, etc.). Said procedure has been implemented...
  • Voom

  • Referenced in 16 articles [sw14009]
  • large body of methodology developed for microarrays. Simulation studies show that voom performs as well...
  • ORIOGEN

  • Referenced in 15 articles [sw07654]
  • instance, during the early days of microarray technology, the number of probes on a cDNA...
  • 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...
  • maSigPro

  • Referenced in 9 articles [sw11024]
  • significantly differential expression profiles in time-course microarray experiments. Motivation: Multi-series time-course microarray ... both a real and a simulated microarray dataset. Availability: The method has been implemented...
  • 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...