• dmGWAS

  • Referenced in 3 articles [sw29291]
  • module searching for genome-wide association studies in protein–protein interaction networks. MOTIVATION: An important ... emerged from the recent success of genome-wide association studies (GWAS) is how to detect ... hold promise for comprehensively examining the interactions between genes underlying the pathogenesis of complex diseases ... datasets into the human protein-protein interaction (PPI) network. The DMS method extensively searches...
  • ARACNE

  • Referenced in 38 articles [sw17200]
  • computational methods for the genome-wide ”reverse engineering” of such networks have been successful only ... lower eukaryotes with simple genomes. Here we present ARACNE, a novel algorithm, using microarray expression ... networks in mammalian cells, yet general enough to address a wider range of network deconvolution ... approach to eliminate the majority of indirect interactions inferred by co-expression methods. Results...
  • NeMoFinder

  • Referenced in 5 articles [sw29732]
  • NeMofinder: genome-wide protein-protein interactions with meso-scale network motifs. Recent works in network...
  • FunCoup

  • Referenced in 1 article [sw27475]
  • FunCoup 3.0: database of genome-wide functional coupling networks. We present an update ... membership in a protein complex and physical interaction. For each of these four classes, several ... Bayesian integration to predict genome-wide functional coupling networks. The FunCoup framework has been completely...
  • GeneFriends

  • Referenced in 1 article [sw41319]
  • regulatory networks. The growing number of genome resequencing efforts and genome-wide association studies often ... need to infer their functions and interaction partners. To facilitate this we have expanded GeneFriends ... obtain from GeneFriends include a co-expression network as well as a summary...
  • netgwas

  • Referenced in 3 articles [sw21512]
  • Package for Network-Based Genome-Wide Association Studies. Graphical models provide powerful tools to model ... widely used in statistics and machine learning particularly to analyze biological networks. In this paper ... construction, reconstructing intra- and inter- chromosomal interactions and exploring high-dimensional genotype-phenotype (and genotypes...
  • MetNet

  • Referenced in 2 articles [sw25662]
  • software in development for analysis of genome-wide RNA, protein and metabolite profiling data ... analyse and model a metabolic and regulatory network map of Arabidopsis, combined with gene expression ... contains a JAVA interface to an interactions database (MetNetDB) containing information on regulatory and metabolic...
  • PIPE

  • Referenced in 6 articles [sw26869]
  • protein interaction networks has received considerable attention in the post-genomic era. The currently available ... biochemical approaches used to detect protein-protein interactions are all time and labour intensive. Consequently ... interactions. Results: Here we explain the development and implementation of a novel Protein-Protein Interaction ... predict protein interactions that are not included in genome-wide yeast TAP tagging projects. Conclusion...
  • NetComm

  • Referenced in 1 article [sw34551]
  • increasingly used to productively analyze genome-wide data. Conventional approaches, such as mean shortest path ... complementary metric. Network communicability considers all paths of all lengths between two network members. Given ... success of previous network analyses of protein–protein interactions, we applied the concepts of network...
  • AutoNet

  • Referenced in 1 article [sw30811]
  • existence of an alternative splicing regulatory network (SRN). The SRN contains a list of gene ... present a methodology to automate genome-wide SRN reconstruction. We construct SRN based ... experimentally verified AS and transcriptional regulatory interaction training set. This SRN reconstruction methodology is demonstrated...
  • LAPACK

  • Referenced in 1713 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • Matlab

  • Referenced in 13702 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 10196 articles [sw00771]
  • R is a language and environment for statistical...
  • PERL

  • Referenced in 274 articles [sw01225]
  • Programming Perl. Perl is a language for easily...
  • BLAS

  • Referenced in 501 articles [sw03216]
  • Low-level utilities common to many mathematical software...
  • SeDuMi

  • Referenced in 1284 articles [sw04002]
  • SeDuMi is a Matlab toolbox for solving optimization...
  • UCI-ml

  • Referenced in 3444 articles [sw04074]
  • UC Irvine Machine Learning Repository. We currently maintain...
  • Bioconductor

  • Referenced in 328 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • SPSS

  • Referenced in 677 articles [sw04269]
  • SPSS is a computer program used for survey...
  • CRAN

  • Referenced in 570 articles [sw04351]
  • R is ‘GNU S’, a freely available language...