• edgeR

  • Referenced in 48 articles [sw06936]
  • package for differential expression analysis of digital gene expression data. t is expected that emerging ... digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many ... fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence ... software package for examining differential expression of replicated count data. An overdispersed Poisson model...
  • impute

  • Referenced in 100 articles [sw14376]
  • data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require ... means clustering are not robust to missing data, and may lose effectiveness even with...
  • BicAT

  • Referenced in 16 articles [sw12371]
  • user interface software for the analysis of gene expression data. It provides five biclustering ... Solaris, Linux and Mac OS. BicAT (Biclustering Analysis Toolbox) is a software tool which offers ... biologists with the analysis and exploration of the gene expression data, e.g. microarrays...
  • DEseq

  • Referenced in 51 articles [sw10344]
  • DESeq: Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence ... count data from high-throughput sequencing assays and test for differential expression based...
  • SynTReN

  • Referenced in 15 articles [sw12311]
  • generator of synthetic gene expression data for design and analysis of structure learning algorithms. Background ... infer the structure of gene regulatory networks based on expression data is an important subject...
  • LCE

  • Referenced in 5 articles [sw25277]
  • cluster ensemble method for improved gene expression data analysis. MOTIVATION: It is far from trivial ... parameterization, for a particular set of gene expression data, because there are a very large...
  • bioNMF

  • Referenced in 6 articles [sw14438]
  • successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even ... specifically perform these types of data analysis in an integrated environment. Results: In this work ... includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature ... sample classification using gene expression. The tool, which is named bioNMF, also contains a user...
  • JIVE

  • Referenced in 12 articles [sw09511]
  • data types, reduces the dimensionality of the data and provides new directions for the visual ... Analysis and has clear advantages over popular two-block methods such as Canonical Correlation Analysis ... Least Squares. A JIVE analysis of gene expression and miRNA data on Glioblastoma Multiforme tumor...
  • EXPANDER

  • Referenced in 8 articles [sw30158]
  • java-based tool for analysis of gene expression and NGS data. It seamlessly integrates ... Identification of differential genes (including methods suitable for NGS data analysis); Clustering and biclustering; Down ... Chromosomal locations; Network-based analysis of the expression data.EXPANDER provides support for analysis of human...
  • TM4

  • Referenced in 12 articles [sw26846]
  • data management and analysis. Microarrays have emerged as the premier tool for studying gene expression ... often challenged by the large quantities of data produced. Well-designed, user-friendly software ... ongoing work in microarray analysis of gene expression, we developed a suite of software that ... major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment...
  • ErmineJ

  • Referenced in 4 articles [sw30047]
  • ErmineJ: Tool for functional analysis of gene expression data sets. Background: It is common ... analysis of functionally-relevant sets of genes in the context of microarray gene expression data ... methods that focus on gene scores or correlation of gene expression profiles. In addition ... gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression...
  • affy

  • Referenced in 35 articles [sw08345]
  • array probe-level data. The software utilities provided with the Affymetrix analysis suite summarize ... makes available only one expression measure for each gene. We have developed this package because ... call them, the probe-level data. We provide some examples demonstrating that having access...
  • ZIFA

  • Referenced in 8 articles [sw32141]
  • inflated single-cell gene expression analysis. Single-cell RNA-seq data allows insight into normal ... gene expression on the single cell level. Dimensionality reduction of such high-dimensional data sets ... essential for visualization and analysis, but single-cell RNA-seq data are challenging for classical...
  • GenMAPP

  • Referenced in 8 articles [sw12317]
  • expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated ... perform a global analysis of gene expression or genomic data in the context of hundreds...
  • GenClust

  • Referenced in 3 articles [sw30045]
  • step in the analysis of gene expression data, and in fact, many classical clustering algorithms ... techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based ... genetic algorithm for clustering gene expression data. It has two key features: (a) a novel...
  • MAANOVA

  • Referenced in 4 articles [sw08357]
  • collection of functions for statistical analysis of gene expression data from two-color cDNA microarray ... assess data quality, apply data transformations, estimate relative gene expression from designed experiments with ANOVA ... differential expression of genes and estimate false-discovery rates, produce graphical summaries of expression patterns ... perform cluster analysis with bootstrapping. The development of MAANOVA was motivated by the need...
  • INCLUSive

  • Referenced in 4 articles [sw17183]
  • algorithms and tools for the analysis of gene expression data and the discovery ... filtering and clustering of microarray data, functional scoring of gene clusters, sequence retrieval, and detection ... reflect a methodology and facilitate complex analysis using different tools. The web services...
  • VarMixt

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

  • Referenced in 1 article [sw34392]
  • Analysis. Algorithms developed for binned data analysis, gene expression data analysis and measurement error models...
  • INMEX

  • Referenced in 4 articles [sw26782]
  • designed to support meta-analysis of multiple gene-expression data sets, as well ... from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module ... flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows ... significant genes can be examined in functional analysis module for enriched Gene Ontology terms...