• BioProspector

  • Referenced in 29 articles [sw09375]
  • regulatory regions of co-expressed genes. The development of high throughput genome sequencing and gene...
  • DEseq

  • Referenced in 60 articles [sw10344]
  • DESeq: Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence ... count data from high-throughput sequencing assays and test for differential expression based...
  • Cytoscape

  • Referenced in 81 articles [sw09080]
  • integrating biomolecular interaction networks with high-throughput expression data and other molecular states into ... network; to visually integrate the network with expression profiles, phenotypes, and other molecular states ... interaction pathways correlating with changes in gene expression, a study of protein complexes involved...
  • CONFAC

  • Referenced in 4 articles [sw35535]
  • integration of comparative genomics with high-throughput gene expression analysis. Here we describe the conserved ... site (CONFAC) software that enables the high-throughput identification of conserved transcription factor binding sites ... regulatory regions of hundreds of genes at a time (http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl). The CONFAC software...
  • oligo

  • Referenced in 9 articles [sw06102]
  • last few years, the high-throughput measurement of gene expressions is the most popular application...
  • DEGseq

  • Referenced in 11 articles [sw07998]
  • identifying differentially expressed genes from RNA-seq data. High-throughput RNA sequencing ... package to identify differentially expressed genes or isoforms for RNA-seq data from different samples...
  • DESeq2

  • Referenced in 27 articles [sw41938]
  • R/Bioconductor package DESeq2: Differential gene expression analysis based on the negative binomial distribution. Estimate variance ... mean dependence in count data from high-throughput sequencing assays and test for differential expression...
  • GENEVESTIGATOR

  • Referenced in 2 articles [sw38837]
  • High-throughput gene expression analysis has become a frequent and powerful research tool in biology...
  • MetNet

  • Referenced in 2 articles [sw25662]
  • network map of Arabidopsis, combined with gene expression profiling data. It contains a JAVA interface ... amounts of data captured by high-throughput gene expression experiments. FCModeler and MetNetDB are currently...
  • JProGO

  • Referenced in 2 articles [sw36932]
  • functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology...
  • Mania

  • Referenced in 1 article [sw10928]
  • high-throughput gene expression data. The algorithm can infer (i) gene-gene interactions from steady ... state expression profiles and (ii) mode-of-action of the components that can trigger changes ... proposed algorithm can identify both information with high performances, thus overcoming the limitation of current...
  • ScanGEO

  • Referenced in 1 article [sw29566]
  • ScanGEO: parallel mining of high-throughput gene expression data. Current options to mine publicly available...
  • PTA

  • Referenced in 1 article [sw09307]
  • genomic medicine. Time-course high-throughput gene expression data are emerging in genomic and translational ... course gene expression data from a group of patients, and identify the genes that make ... course signal recovery and feature selection with high-dimensional data. Moreover, PTA derives new insights...
  • MultiCluster

  • Referenced in 6 articles [sw30715]
  • individual gene expression data using semi-nonnegative tensor decomposition. The advent of high-throughput sequencing ... gene expression measurements across different tissues and individuals. In this setting, variation in expression levels ... arises due to contributions specific to genes, tissues, individuals, and interactions thereof. Classical clustering methods ... projection procedure which detects covariate-related genes with high power, demonstrating the advantage of tensor...
  • dtangle

  • Referenced in 2 articles [sw40223]
  • Type Deconvolution from Gene Expressions. Deconvolving cell types from high-throughput gene profiling data...
  • gaga

  • Referenced in 4 articles [sw06101]
  • model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification...
  • leapp

  • Referenced in 11 articles [sw11213]
  • primary projection. These functions take a gene expression value matrix, a primary covariate vector ... used as a general tool for high throughput data sets where dependence may be involved...
  • kerfdr

  • Referenced in 5 articles [sw35302]
  • different high-throughput biological data such as patterns in DNA sequences, genes expression and genome...
  • OSG-KINC

  • Referenced in 1 article [sw29629]
  • throughput gene co-expression network construction using the open science grid. Gene Co-expression Network ... datasets available for mining complex gene expression patterns, novel algorithms and computational frameworks must ... KINC is a Pegasus workflow that enables highly parallel execution of KINC - Knowledge Independent Network...
  • MMG

  • Referenced in 4 articles [sw29328]
  • expressed, rather than which genes. Furthermore, in many interesting cases (such as high-throughput proteomics ... novel probabilistic model to identify differentially expressed submodules of biological networks and pathways. The method...