• BioProspector

  • Referenced in 29 articles [sw09375]
  • upstream region of genes in the same gene expression pattern group and looks for regulatory ... input sequences to contain zero to multiple copies of the motif. In addition, BioProspector...
  • maskmeans

  • Referenced in 1 article [sw35561]
  • Atlas, where multiple molecular profiles (gene expression, microRNA expression, methylation and copy number alterations...
  • SGN Sim

  • Referenced in 8 articles [sw29325]
  • simulation algorithm (SSA) able to deal with multiple time delayed events. The delays ... chemical reactions. Perturbations, e.g. gene deletion, over-expression, copy and mutation, can be modeled...
  • DINGO

  • Referenced in 2 articles [sw29317]
  • consideration of relationships that are conserved across multiple groups. Method: We propose a pathway-based ... Genome Atlas. The hub genes found by mRNA expression, DNA copy number, methylation and microRNA...
  • MulRF

  • Referenced in 2 articles [sw23051]
  • infer species trees from incongruent multi-copy gene trees using a generalization of the Robinson ... following additional features: Weighted input gene trees for species tree search. Topological constraints ... inferred species tree. Automated execution of multiple replicates of tree search heuristic. MulRF distance...
  • rmscca

  • Referenced in 1 article [sw23317]
  • grouped together, thus better understanding multiple interactions that are otherwise difficult to compute or grasp ... discover, for example, relationships between gene expression and gene copy number variation ... Additionally, we have used SCCA to find multiple canonical pairs for extended knowledge about...
  • FISHtrees

  • Referenced in 1 article [sw29659]
  • FISH) make it feasible to detect multiple copy-number changes in hundreds of cells ... that model changes in ploidy and individual gene copy-number variations. We present FISHtrees ... changes of a single gene into trees modeling changes in multiple genes and the ploidy...
  • ParticleMDI

  • Referenced in 1 article [sw35255]
  • where observational units have data arising from multiple sources. Our approach uses a particle Gibbs ... Genome Atlas, for which there are gene expression, copy number variation, DNA methylation, protein expression...
  • fcros

  • Referenced in 0 articles [sw17070]
  • search for differentially expressed genes and to detect recurrent chromosomal copy number aberrations. This method ... dataset and there is no problem of multiple tests when using this method. For aCGH...
  • R

  • Referenced in 8776 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1741 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • TSPLIB

  • Referenced in 674 articles [sw00983]
  • TSPLIB is a library of sample instances for...
  • Bioconductor

  • Referenced in 307 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • ape

  • Referenced in 57 articles [sw04569]
  • R package ape: Analyses of Phylogenetics and Evolution...
  • Genocop

  • Referenced in 1083 articles [sw04707]
  • Genocop, by Zbigniew Michalewicz, is a genetic algorithm...
  • gcrma

  • Referenced in 96 articles [sw06104]
  • Bioconductor/R package gcrma: Background Adjustment Using Sequence Information...
  • fastDNAml

  • Referenced in 91 articles [sw06651]
  • fastDNAml is a program for estimating maximum likelihood...
  • edgeR

  • Referenced in 49 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis...
  • SemiPar

  • Referenced in 705 articles [sw07116]
  • R package SemiPar: Semiparametic Regression. The primary aim...