• PermutMatrix

  • Referenced in 12 articles [sw22075]
  • PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. PermutMatrix ... hierarchical clustering for gene expression data...
  • LAS

  • Referenced in 17 articles [sw17180]
  • three-part validation study using two gene expression data sets. The validation study examines quantitative...
  • SynTReN

  • Referenced in 14 articles [sw12311]
  • SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning ... infer the structure of gene regulatory networks based on expression data is an important subject...
  • TM4

  • Referenced in 11 articles [sw26846]
  • premier tool for studying gene expression on a genomic scale. Advances in the precision ... ongoing work in microarray analysis of gene expression, we developed a suite of software that...
  • iSS-PseDNC

  • Referenced in 15 articles [sw22438]
  • together are essential processes in eukaryotic gene expression. With the avalanche of genome sequences generated ... splice sites that play important roles in gene structure annotation and even in RNA splicing...
  • iTIS-PseTNC

  • Referenced in 15 articles [sw22449]
  • Translation is a key process for gene expression. Timely identification of the translation initiation site...
  • GEOquery

  • Referenced in 9 articles [sw17285]
  • GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Microarray technology has become ... treatment conditions and disease states. The Gene Expression Omnibus (Barrett et al., 2005), developed ... repository of nearly 140 000 gene expression experiments. The BioConductor project (Gentleman...
  • maSigPro

  • Referenced in 9 articles [sw11024]
  • maSigPro: A method to identify significantly differential expression profiles in time-course microarray experiments. Motivation ... researcher is frequently interested in studying gene expression changes along time and in evaluating trend ... identify genes that show different gene expression profiles across analytical groups in time-course experiments ... defined variables to identify differentially expressed genes, and in second a variable selection strategy...
  • pSumo-CD

  • Referenced in 14 articles [sw23949]
  • biological processes such as replicating genome, expressing gene, localizing and stabilizing proteins; unfortunately...
  • twilight

  • Referenced in 9 articles [sw06103]
  • typical microarray setting with gene expression data observed under two conditions, the local false discovery ... describes the probability that a gene is not differentially expressed between the two conditions given ... clear differential and clear non-differential gene expression. Package twilight contains two main functions: Function...
  • EDGE

  • Referenced in 9 articles [sw13105]
  • EDGE: extraction and analysis of differential gene expression. Summary: EDGE (Extraction of Differential Gene Expression...
  • HykGene

  • Referenced in 9 articles [sw23981]
  • 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. A major problem ... classification is that the number of features (genes) greatly exceeds the number of instances (tissue...
  • BGX

  • Referenced in 14 articles [sw06935]
  • posterior distribution for the expression of each gene. Moreover, BGX can take into account probe ... analyse the results, such as ranking genes by expression level as well as statistically based ... amount of up and down regulated genes between two conditions...
  • STOCKS

  • Referenced in 13 articles [sw10438]
  • applicable to the study of prokaryotic gene expression. Features dedicated to the study of cellular...
  • JIVE

  • Referenced in 12 articles [sw09511]
  • Least Squares. A JIVE analysis of gene expression and miRNA data on Glioblastoma Multiforme tumor...
  • affy

  • Referenced in 33 articles [sw08345]
  • makes available only one expression measure for each gene. We have developed this package because ... improvements to quality control assessments, normalization, and expression measures. The software is implemented...
  • BioPortal

  • Referenced in 12 articles [sw22917]
  • biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through...
  • iDNA-Methyl

  • Referenced in 19 articles [sw22423]
  • modify their DNAs to change the expression of gene products. It plays very important roles...
  • oligo

  • Referenced in 8 articles [sw06102]
  • years, the high-throughput measurement of gene expressions is the most popular application of microarray ... improve accuracy and precision of the gene expression measurements, relative to ad hoc procedures introduced ... identification of DNA sequence variants in specific genes or regions of the human genome that...
  • iEnhancer-EL

  • Referenced in 11 articles [sw27668]
  • play a critical role in controlling gene expression. Although some bioinformatics tools were developed, they...