• REDUCE

  • Referenced in 738 articles [sw00789]
  • forms; automatic and user controlled simplification of expressions; calculations with symbolic matrices; arbitrary precision integer ... functions and extending program syntax; analytic differentiation and integration; factorization of polynomials; facilities ... algebraic equations; facilities for the output of expressions in a variety of formats; facilities...
  • Maxima

  • Referenced in 144 articles [sw00560]
  • manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential...
  • INTOPT_90

  • Referenced in 304 articles [sw04705]
  • chapter about non-differentiable problems (17 pages) studies function expressions containing if-then-else connectives...
  • edgeR

  • Referenced in 44 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ... fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence ... Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model...
  • DEseq

  • Referenced in 48 articles [sw10344]
  • DESeq: Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence ... throughput sequencing assays and test for differential expression based on a model using the negative...
  • Janet

  • Referenced in 34 articles [sw07776]
  • number of tools for dealing with differential expressions and differential operators. A generic linearization ... computed. Some procedures translate differential expressions into jet notation and vice versa. For the Weyl...
  • limma

  • Referenced in 48 articles [sw10458]
  • Data. A survey is given of differential expression analyses using the linear modeling features...
  • GSA

  • Referenced in 37 articles [sw18747]
  • paper discusses the problem of identifying differentially expressed groups of genes from a microarray experiment...
  • UFL

  • Referenced in 47 articles [sw11183]
  • variational forms and functionals, automatic differentiation of forms and expressions, arbitrary function space hierarchies ... multifield problems, general differential operators and flexible tensor algebra. With these features, UFL has been ... effortlessly express finite element methods for complex systems of partial differential equations in near-mathematical...
  • EBarrays

  • Referenced in 31 articles [sw08355]
  • developed an empirical Bayes methodology for gene expression data to account for replicate arrays, multiple ... calculate posterior probabilities of patterns of differential expression across multiple conditions. This chapter provides...
  • BaySeq

  • Referenced in 17 articles [sw10343]
  • Empirical Bayesian analysis of patterns of differential expression in count data. Results: We propose ... framework for defining patterns of differential expression and develop a novel algorithm, baySeq, which uses ... approach to detect these patterns of differential expression within a set of sequencing samples...
  • SAM

  • Referenced in 20 articles [sw08356]
  • False Discovery Rates for Detecting Differential Gene Expression in DNA Microarrays. SAM is a computer ... package for correlating gene expression with an outcome parameter such as treatment, survival time ... general approach to detecting differential gene expression in DNA microarrays. Some recently developed methodology...
  • multtest

  • Referenced in 20 articles [sw08262]
  • procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments...
  • GeneRank

  • Referenced in 16 articles [sw27064]
  • based on the fold-change of gene expression between a reference and a ”treated” sample ... results usually combines lists of differentially expressed genes with previous knowledge about their biological function...
  • DEGseq

  • Referenced in 11 articles [sw07998]
  • DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. High-throughput ... DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data...
  • EDGE

  • Referenced in 9 articles [sw13105]
  • EDGE: extraction and analysis of differential gene expression. Summary: EDGE (Extraction of Differential Gene Expression ... perform both standard and time course differential expression analysis. The functions are based on newly...
  • recount

  • Referenced in 9 articles [sw17315]
  • used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder ... perform annotation-agnostic differential expression analyses with the data from the recount project as described...
  • maSigPro

  • Referenced in 9 articles [sw11024]
  • maSigPro: A method to identify significantly differential expression profiles in time-course microarray experiments. Motivation ... 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...
  • twilight

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

  • Referenced in 21 articles [sw16033]
  • errors, and symbolic differentiation, which is affected by expression swell and cannot fully handle algorithmic ... control flow. Using the DiffSharp library, differentiation (gradients, Hessians, Jacobians, directional derivatives, and matrix-free ... full expressive capability of the language including control flow. DiffSharp allows composition of differentiation using...