• MDR

  • Referenced in 9 articles [sw22494]
  • gene-environment interactions. Motivation: Polymorphisms in human genes are being described in remarkable numbers. Determining ... because the effect of any single genetic variation will ... likely be dependent on other genetic variations (genegene interaction or epistasis) and environmental factors...
  • RoVerGeNe

  • Referenced in 13 articles [sw10954]
  • dynamical properties of gene networks with respect to parameter variations and for the tuning...
  • GSVA

  • Referenced in 3 articles [sw17293]
  • GSVA: gene set variation analysis for microarray and RNA-seq data. Background: Gene set enrichment ... address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates...
  • GeneRank

  • Referenced in 16 articles [sw27064]
  • usually based on the fold-change of gene expression between a reference and a ”treated ... genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous...
  • Noisy

  • Referenced in 5 articles [sw21022]
  • sites. As most protein-coding genes show dramatic variations in substitution rates that...
  • MAST

  • Referenced in 5 articles [sw30709]
  • source of nuisance variation. Our model provides gene set enrichment analysis tailored to single-cell...
  • ANOSVA

  • Referenced in 2 articles [sw35536]
  • detecting splice variation from expression data. Many or most mammalian genes undergo alternative splicing, generating ... transcripts from a single gene. New information on splice variation is becoming available through technology ... junctions per gene. We have developed a statistical method, ANalysis Of Splice VAriation (ANOSVA ... genes with evidence of tissue-specific splice variation...
  • MultiCluster

  • Referenced in 3 articles [sw30715]
  • this setting, variation in expression levels arises due to contributions specific to genes, tissues, individuals ... decomposition which permits the investigation of transcriptome variation across individuals and tissues simultaneously. We further ... tensor projection procedure which detects covariate-related genes with high power, demonstrating the advantage...
  • DriverFinder

  • Referenced in 1 article [sw34273]
  • integrating somatic mutations, copy number variations, gene-gene interaction network, tumor expression, and normal expression...
  • PathRacer

  • Referenced in 1 article [sw29679]
  • sequences of antibiotic resistance genes, or allelic variations amongst highly conserved housekeeping genes used...
  • DRIMSeq

  • Referenced in 1 article [sw25781]
  • characterize the effects of genetic variation on gene expression. RNA sequencing (RNA-seq) has provided...
  • qtl

  • Referenced in 4 articles [sw20320]
  • crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits...
  • GenePattern

  • Referenced in 4 articles [sw16895]
  • analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow...
  • ChromoScan

  • Referenced in 3 articles [sw35412]
  • genetic associations with disease, gene expression profiles, DNA copy number variations, as well as other...
  • MISA

  • Referenced in 3 articles [sw13359]
  • been chosen to capture variation in a set of related genes, such as those involved...
  • JIVE

  • Referenced in 12 articles [sw09511]
  • noise. JIVE quantifies the amount of joint variation between data types, reduces the dimensionality ... Partial Least Squares. A JIVE analysis of gene expression and miRNA data on Glioblastoma Multiforme...
  • rmscca

  • Referenced in 1 article [sw23317]
  • relationships between gene expression and gene copy number variation. One of the biggest problems...
  • Siconos

  • Referenced in 10 articles [sw25724]
  • Digital converter. Sliding mode control systems. Biology (Gene regulatory network). Other applications are found ... with state constraints), Optimization (Complementarity systems and Variational inequalities), Fluid Mechanics, and Computer Graphics...
  • globalGSA

  • Referenced in 1 article [sw11115]
  • Association Studies. Implementation of three different Gene set analysis (GSA) algorithms for combining the individual ... genetic variats (SNPs) in a gene level pvalue. The implementation includes the selection...
  • SNPs3D

  • Referenced in 5 articles [sw30035]
  • SNPs3D: Candidate gene and SNP selection for association studies. Background: The relationship between disease susceptibility ... genetic variation is complex, and many different types of data are relevant. We describe ... three primary modules. One module identifies which genes are candidates for involvement in a specified...