• impute

  • Referenced in 104 articles [sw14376]
  • gene array values as input. For example, methods such as hierarchical clustering and K-means ... clustering are not robust to missing data, and may lose effectiveness even with ... estimation of missing values in gene microarray data. We implemented and evaluated three methods...
  • COSA

  • Referenced in 52 articles [sw22936]
  • clustering on a small subset of variables are discussed. Applications in different domains, including gene...
  • clusterProfiler

  • Referenced in 8 articles [sw28862]
  • functional profiles for genes and gene clusters. This package implements methods to analyze and visualize ... KEGG) of gene and gene clusters...
  • NEURON

  • Referenced in 187 articles [sw03059]
  • spike patterns exhibits superlinear speedup on Beowulf clusters and demonstrates that spike communication overhead ... speed cache. On the EPFL IBM Blue Gene, almost linear speedup was obtained...
  • HykGene

  • Referenced in 9 articles [sw23981]
  • novel hybrid approach that combines gene ranking and clustering analysis. In this approach, we first ... genes, and then applied hierarchical clustering on these genes to generate a dendrogram. Finally ... line algorithm and marker genes are selected by collapsing dense clusters. Empirical study using three ... capable of selecting relatively few marker genes while offering the same or better leave...
  • OSCAR

  • Referenced in 55 articles [sw03026]
  • Simultaneous regression shrinkage, variable selection, and supervised clustering of predictors with OSCAR. Variable selection ... gene expression data. In this article, a new method, called OSCAR (octagonal shrinkage and clustering...
  • ClueGO

  • Referenced in 9 articles [sw22916]
  • redundant biological terms for large clusters of genes in a functionally grouped network. The identifiers ... extended by the user. ClueGO performs single cluster ... analysis and comparison of several clusters (lists of genes). From the ontology sources used ... genes. On the network, the node colour can be switched between functional groups and clusters...
  • PermutMatrix

  • Referenced in 13 articles [sw22075]
  • PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. PermutMatrix ... dataset. It implements several types of cluster analysis and a variety of methods for statistical ... work on the use of hierarchical clustering for gene expression data...
  • OrthoMCL

  • Referenced in 15 articles [sw29602]
  • larger genomes may contain multiple paralogous genes, and sequence information is often incomplete. OrthoMCL provides ... across multiple eukaryotic taxa, using a Markov Cluster algorithm to group (putative) orthologs and paralogs ... cluster orthologs from multiple species. OrthoMCL clusters are coherent with groups identified ... www.cbil.upenn.edu/gene-family). Analysis of clusters incorporating P. falciparum genes identifies numerous enzymes that were incompletely...
  • CLIFF

  • Referenced in 10 articles [sw35898]
  • present CLIFF, an algorithm for clustering biological samples using gene expression microarray data. This clustering ... data, the high dimensionality of the feature (gene) space, and the fact that many features ... between two computational processes, feature filtering and clustering. Given a reference partition that approximates ... samples and 7130 genes, we demonstrate that CLIFF outperforms standard clustering approaches that...
  • SSS

  • Referenced in 34 articles [sw07794]
  • parallel computation using cluster computers. We discuss an example from gene expression cancer genomics, comparisons...
  • GenClust

  • Referenced in 4 articles [sw30045]
  • GenClust: A genetic algorithm for clustering gene expression data. Background: Clustering is a key step ... analysis of gene expression data, and in fact, many classical clustering algorithms are used ... genetic algorithm for clustering gene expression data. It has two key features: (a) a novel ... methodology, specifically conceived for validating clusters of gene expression data. The validity of GenClust...
  • LCE

  • Referenced in 5 articles [sw25277]
  • link-based cluster ensemble method for improved gene expression data analysis. MOTIVATION ... most effective clustering method and its parameterization, for a particular set of gene expression data ... gene expression and synthetic datasets indicate that LCE: (i) usually outperforms the existing cluster ensemble ... computationally efficient for large datasets and gene clustering. AVAILABILITY: Online supplementary and implementation are available...
  • GOSim

  • Referenced in 5 articles [sw08204]
  • These can e.g. be used to cluster genes according to their biological function. Vice versa...
  • ECgene

  • Referenced in 4 articles [sw17328]
  • ECgene: genome-based EST clustering and gene modeling for alternative splicing. With the availability ... alignment, genome-based EST clustering became a viable method for gene modeling. We developed ... novel gene-modeling method, ECgene (Gene modeling by EST Clustering), which combines genome-based ... each cluster are subclustered further according to the compatibility with gene structure of each splice...
  • clusterRepro

  • Referenced in 7 articles [sw13741]
  • package clusterRepro: Reproducibility of gene expression clusters. A function for validating microarry clusters via reproducibility...
  • INCLUSive

  • Referenced in 4 articles [sw17183]
  • algorithms and tools for the analysis of gene expression data and the discovery ... elements. The tools allow normalization, filtering and clustering ... microarray data, functional scoring of gene clusters, sequence retrieval, and detection of known and unknown...
  • BUCKy

  • Referenced in 7 articles [sw23619]
  • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Motivation: BUCKy is a C++ program ... method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary...
  • CONFAC

  • Referenced in 4 articles [sw35535]
  • significantly enriched in promoters of gene clusters from microarray analyses compared to sets of unchanging...
  • gaga

  • Referenced in 4 articles [sw06101]
  • analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample...