• PDESpecialSolutions

  • Referenced in 60 articles [sw12342]
  • Symbolic computation of exact solutions expressible in hyperbolic and elliptic functions for nonlinear PDEs. Algorithms ... form solutions of nonlinear ordinary and partial differential equations (ODEs and PDEs). New algorithms...
  • Sacado

  • Referenced in 8 articles [sw06602]
  • templates for operator overloading-based automatic differentiation Expression templates are a well-known ... operator overloading-based forward mode automatic differentiation schemes in the C++ programming ... language by translating the differentiation from individual operators to whole expressions. However standard expression template ... efficiency of expression templates and their implementation in the automatic differentiation package { t Sacado...
  • AceGen

  • Referenced in 32 articles [sw10821]
  • Mathematica, automatic differentiation technique, automatic code generation and simultaneous optimization of expressions. The multi-language...
  • SMS

  • Referenced in 29 articles [sw01085]
  • finite-element code by simultaneous optimization of expressions. The paper presents a MATHEMATICA package ... capabilities of Mathematica, automatic differentiation technique, simultaneous optimization of expressions and a stochastic evaluation...
  • RankProd

  • Referenced in 6 articles [sw07961]
  • RankProd: Rank Product method for identifying differentially expressed genes with application in meta-analysis ... parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated...
  • gprege

  • Referenced in 6 articles [sw31093]
  • Gaussian Process Ranking and Estimation of Gene Expression time-series. The gprege package implements ... simple approach to ranking differentially expressed gene expression time-courses through Gaussian process regression ... hypotheses acts as a score of differential expression for the profile. Comparison via ROC curves...
  • MMG

  • Referenced in 4 articles [sw29328]
  • abundance, enzyme concentrations, etc.) which are differentially expressed in two different conditions. Popular approaches involve ... pertinent question is which subnetworks are differentially expressed, rather than which genes. Furthermore, in many ... novel probabilistic model to identify differentially expressed submodules of biological networks and pathways. The method ... strategy to infer posterior probabilities of differential expression, as well as posterior probabilities over...
  • EBSeq

  • Referenced in 7 articles [sw17161]
  • Motivation: Messenger RNA expression is important in normal development and differentiation, as well ... experiments allow for the identification of differentially expressed (DE) genes and their corresponding isoforms...
  • QuasiSeq

  • Referenced in 7 articles [sw11359]
  • Count Tables Using Quasi-likelihood. Identify differentially expressed genes in RNA-seq count data using...
  • ROAST

  • Referenced in 7 articles [sw17318]
  • gene set test is a differential expression analysis in which a P-value is assigned...
  • HTSeq

  • Referenced in 7 articles [sw16898]
  • that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads...
  • gaga

  • Referenced in 4 articles [sw06101]
  • parsimonious and flexible model for differential expression analysis Bioconductor version: Release (2.10) Implements the GaGa ... high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally...
  • CAMERA

  • Referenced in 4 articles [sw30339]
  • particular gene annotation category amongst the differential expression results from a microarray experiment. Existing gene ... retains excellent power for detecting genuine differential expression. Analysis of breast cancer data shows that...
  • Theano

  • Referenced in 64 articles [sw05894]
  • define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Theano features tight integration ... transparent use of a GPU, efficient symbolic differentiation, speed and stability optimizations, dynamic C code...
  • CoXpress

  • Referenced in 3 articles [sw17858]
  • CoXpress: differential co-expression in gene expression data. Background: Traditional methods of analysing gene expression ... include a statistical test to find differentially expressed genes, or use of a clustering algorithm ... miss groups of genes which form differential co-expression patterns under different subsets of experimental ... identify groups of genes that are differentially co-expressed. Results: We have developed coXpress...
  • TWILIGHT

  • Referenced in 9 articles [sw06788]
  • Local False Discovery Rate Screening for differential gene expression in microarray studies leads to difficult...
  • colcor

  • Referenced in 5 articles [sw12289]
  • control groups and we could seek differentially expressed genes. The empirical...
  • lpc

  • Referenced in 5 articles [sw11217]
  • settings. In particular, we test for differentially-expressed genes in a microarray experiment. We wish...
  • sva

  • Referenced in 5 articles [sw21306]
  • effects and using surrogate variables in differential expression analysis have been shown to reduce dependence...
  • DEXUS

  • Referenced in 2 articles [sw23833]
  • DEXUS: Identifying differential expression in RNA-Seq studies with unknown condtions. Detection of differential expression ... project. We present DEXUS for detecting differential expression in RNA-Seq data for which ... condition. A transcript is considered differentially expressed if modeling of its read counts requires more ... noise and variation due to differential expression. Evidence of differential expression is measured...