• Mathematica

  • Referenced in 5883 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • R

  • Referenced in 8359 articles [sw00771]
  • R is a language and environment for statistical...
  • Graphviz

  • Referenced in 81 articles [sw01283]
  • Graphviz is open source graph visualization software. Graph...
  • Bioconductor

  • Referenced in 298 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • gplots

  • Referenced in 6 articles [sw04555]
  • gplots: Various R Programming Tools for Plotting Data...
  • PLINK

  • Referenced in 61 articles [sw04581]
  • PLINK is a free, open-source whole genome...
  • LIBSVM

  • Referenced in 1088 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • gcrma

  • Referenced in 95 articles [sw06104]
  • Bioconductor/R package gcrma: Background Adjustment Using Sequence Information...
  • edgeR

  • Referenced in 46 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis...
  • igraph

  • Referenced in 150 articles [sw07066]
  • The igraph software package for complex network research...
  • WGCNA

  • Referenced in 17 articles [sw07123]
  • R package WGCNA: Weighted Correlation Network Analysis. Functions...
  • BoolNet

  • Referenced in 14 articles [sw07365]
  • BoolNet: Generation, reconstruction, simulation and analysis of synchronous...
  • Cytoscape

  • Referenced in 69 articles [sw09080]
  • Cytoscape: A Software Environment for Integrated Models of...
  • COPASI

  • Referenced in 62 articles [sw12253]
  • COPASI: biochemical network simulator. COPASI is a software...
  • Dynagraph

  • Referenced in 13 articles [sw13656]
  • The Dynagraph libraries are written in platform-neutral...
  • BioNet

  • Referenced in 5 articles [sw13828]
  • The BioNet package provides an extensive framework for...
  • KEGG

  • Referenced in 252 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG...
  • Python

  • Referenced in 1378 articles [sw14460]
  • Python is a widely used high-level, general...
  • RedeR

  • Referenced in 2 articles [sw14646]
  • RedeR: R/Bioconductor package for representing modular structures, nested...
  • Cellnoptr

  • Referenced in 5 articles [sw15114]
  • CellNOpt (from CellNetOptimizer; a.k.a. CNO) is a software...