• mixOmics

  • Referenced in 26 articles [sw09508]
  • transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, mixOmics...
  • Oncomine

  • Referenced in 7 articles [sw17289]
  • applied to cancer transcriptome analysis; however, the majority of such data are not easily accessible ... analytic approaches have been applied to microarray analysis; however, their application is often limited ... delivering cancer transcriptome data to the biomedical research community. Our analysis has identified the genes...
  • MSEA

  • Referenced in 2 articles [sw16938]
  • widely used technique in transcriptomic data analysis that uses a database of predefined gene sets ... understanding transcriptomic data, no similar tools are currently available for understanding metabolomic data. Here ... based server, called Metabolite Set Enrichment Analysis (MSEA), to help researchers identify and interpret patterns...
  • MATHT

  • Referenced in 1 article [sw27453]
  • MATHT: a web server for comprehensive transcriptome data analysis. The current software/algorithms for high-throughput ... sequence data analysis are not user-friendly. We developed MATHT, the Multifaceted Analysis Tool ... transcriptome data. The web server provides modules for data preprocessing, differential expression analysis, dataset integration ... server that provides comprehensive analysis of transcriptome data, especially integration analysis using special standardization across...
  • PathCellNet

  • Referenced in 2 articles [sw29377]
  • types by performing a comparative analysis of transcriptomic data. Particularly, we integrate transcriptomic datasets measuring...
  • iBATCGH

  • Referenced in 1 article [sw19388]
  • iBATCGH: integrative Bayesian analysis of transcriptomic and CGH data. We describe a method ... package for the integrative analysis of transcriptomic and genomic data, based on a hierarchical Bayesian...
  • ARSyN

  • Referenced in 2 articles [sw09280]
  • noise in multifactorial time course microarray experiments. Transcriptomic profiling experiments that aim to the identification ... factors and their interactions on gene expression. Data from these controlled experiments, however, may also ... models, and hamper data analysis. Commonly, normalization methods are applied to transcriptomics data to remove ... microarray data that takes into account these 2 last aspects. By combining analysis of variance...
  • integrOmics

  • Referenced in 4 articles [sw28007]
  • omics’ data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple ... analysis is a major computational and technical challenge as most approaches suffer from high data...
  • BioNet

  • Referenced in 5 articles [sw13828]
  • analysis using R and BioConductor. It includes the statistics for the integration of transcriptomic ... functional data with biological networks, the methods for scoring of nodes, methods for optimal, suboptimal...
  • GSAASeqSP

  • Referenced in 1 article [sw25397]
  • toolset for gene set association analysis of RNA-Seq data. RNA-Seq is quickly becoming ... comprehensively characterizing whole transcriptome activity, and the analysis of count data from RNA-Seq requires...
  • Metabox

  • Referenced in 1 article [sw28994]
  • analysis, functional analysis and integrative exploration of metabolomic data within proteomic and transcriptomic contexts. With ... each analysis module, it also supports data analysis of other ‘omic’ families. The toolbox...
  • NGS-Trex

  • Referenced in 1 article [sw17151]
  • Data. RNA-Seq technology allows the rapid analysis of whole transcriptomes taking advantage of next ... analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding ... analysis workflow. Used through a web interface, NGS-Trex processes data and profiles the transcriptome...
  • curatedOvarianData

  • Referenced in 3 articles [sw17291]
  • transcriptome. This article introduces a manually curated data collection for gene expression meta-analysis ... designs, expression data processing methods and clinical data formats. We confirm that the recently proposed ... debulking, which was possible only through meta-analysis owing to insufficient sample sizes ... clinically oriented investigation of the ovarian cancer transcriptome. The package and pipeline for producing...
  • Puma

  • Referenced in 4 articles [sw19121]
  • propagating uncertainty in microarray analysis. Most analyses of Affymetrix GeneChip data (including tranditional 3’ arrays ... exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels...
  • MoNeRe

  • Referenced in 1 article [sw28180]
  • This enables a platform both for quantitative analysis of networked regression, but also testing ... vivo transcriptomic data. Data generated from the model, using flux balance analysis to construct...
  • COVAIN

  • Referenced in 1 article [sw10556]
  • also be used for other omics data analysis. A C language programming module was integrated ... datasets, e.g., genome-level proteomics and transcriptomics data sets which usually contain several thousand ... more variables. COVAIN can perform cross analysis and integration between several datasets, which might...
  • BioMet

  • Referenced in 1 article [sw20501]
  • resource for stoichiometric analysis and for integration of transcriptome and interactome data, thereby exploiting...
  • SequentialMA

  • Referenced in 1 article [sw10526]
  • analysis for microarray data based on sensitivity and meta-analysis. Transcriptomic studies using microarray technology ... context of clinical trials, for microarray analysis. Through interim analyses at different stages ... already. par The high dimensionality of microarray data facilitates the sequential approach. Since thousands...
  • BABAR

  • Referenced in 1 article [sw18997]
  • transcriptomic data to be readily compared and re-analysed in the light of new data ... Excellent software exists for the normalisation and analysis of microarray data but many data have ... with the microarray data in excellent agreement with RT-PCR analysis. When applied ... differentially expressed genes or network inference analysis from transcriptomic datasets...
  • ParaKMeans

  • Referenced in 4 articles [sw29731]
  • transcriptome of many biological systems has generated an enormous amount of data. A common technique ... organize and analyze microarray data is to perform cluster analysis. While many clustering algorithms have...