• edgeR

  • Referenced in 41 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 44 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...
  • EDGE

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

  • Referenced in 9 articles [sw17315]
  • ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. Explore ... used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder...
  • ROAST

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

  • Referenced in 6 articles [sw16898]
  • exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However ... that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads...
  • BaySeq

  • Referenced in 16 articles [sw10343]
  • baySeq: Empirical Bayesian analysis of patterns of differential expression in count data. Results: We propose...
  • CAMERA

  • Referenced in 4 articles [sw30339]
  • analysis to test for enrichment of a particular gene annotation category amongst the differential expression ... retains excellent power for detecting genuine differential expression. Analysis of breast cancer data shows that...
  • sva

  • Referenced in 4 articles [sw21306]
  • package SVA: Surrogate Variable Analysis. The sva package contains functions for removing batch effects ... effects and using surrogate variables in differential expression analysis have been shown to reduce dependence...
  • DCGL

  • Referenced in 2 articles [sw17704]
  • package DCGL: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data ... filtration; 2) link filtration; 3) differential co-expression analysis: DCG (Differential Coexpressed Gene) identification...
  • RankProd

  • Referenced in 5 articles [sw07961]
  • method for identifying differentially expressed genes with application in meta-analysis. Non-parametric method ... identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false ... combine data sets from different origins (meta-analysis) to increase the power of the identification...
  • VarMixt

  • Referenced in 5 articles [sw21100]
  • variance modelling for the differential analysis of replicated gene expression data. MOTIVATION: Identifying differentially regulated ... step in the microarray data analysis process. Many different approaches and methodological developments have been...
  • compcodeR

  • Referenced in 1 article [sw23834]
  • data. Bioconductor: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods ... results obtained by different methods for differential expression analysis of RNAseq data. It also contains ... several packages for performing the differential expression analysis...
  • joda

  • Referenced in 2 articles [sw20391]
  • Joint Deregulation Analysis (JODA). joda is an R package implementing the JODA algorithm introduced ... three steps: (1) Computing probabilities of differential expression of the genes in the perturbation experiments ... examples of differential genes. The differential expression analysis is performed using our approach implemented ... average of the probabilities of differential expression over those perturbation experiments that affect this regulator...
  • PROPER

  • Referenced in 2 articles [sw17314]
  • evaluating the statistical power in differential expression analysis from RNA-seq data...
  • contamDE

  • Referenced in 1 article [sw31459]
  • contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples. Accurate detection ... differentially expressed genes between tumor and normal samples is a primary approach of cancer-related ... infiltration of tumor surrounding normal cells, the expression data derived from tumor samples would always ... being, there does not exists any differential expression analysis approach for RNA-seq data...
  • GSA

  • Referenced in 35 articles [sw18747]
  • paper discusses the problem of identifying differentially expressed groups of genes from a microarray experiment ... point is the interesting Gene Set Enrichment Analysis (GSEA) procedure of {it A. Subramanian...
  • SMS

  • Referenced in 23 articles [sw01085]
  • finite-element code by simultaneous optimization of expressions. The paper presents a MATHEMATICA package ... formulas needed in nonlinear finite element analysis. Symbolic generation of the characteristic arrays of nonlinear ... capabilities of Mathematica, automatic differentiation technique, simultaneous optimization of expressions and a stochastic evaluation ... then incorporated into an existing finite element analysis environment. SMS was already used to developed...
  • RoVerGeNe

  • Referenced in 13 articles [sw10954]
  • Networks. Rovergene is a tool for the analysis of genetic regulatory networks under parameter uncertainty ... class of piecewise multiaffine differential equation models, dynamical properties are expressed in linear temporal logic ... intervals. The tool addresses two problems: robustness analysis: checking whether a dynamical property is satisfied...