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Editor: hamrhein
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Editor: diane
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  * [[http://networkx.lanl.gov/ | Network X]], python graph library
  * [[http://networkx.lanl.gov/pygraphviz/ | PyGraphViz]], python bridge to graphviz
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  * [[http://matplotlib.sourceforge.net | matplotlib ]], python plotting library
  * [[http://numpy.scipy.org | NumPy ]], python scientific computing package
  * Python packages
   * [[http://matplotlib.sourceforge.net | matplotlib ]], python plotting library
   * [[http://numpy.scipy.org | NumPy ]], python scientific computing package
    * [[http://networkx.lanl.gov/ | Network X]], python graph library
    * [[http://networkx.lanl.gov/pygraphviz/ | PyGraphViz]], python bridge to graphviz

Installed Software

Information about the extra software packages we have installed.

  • samtools, SAM/BAM file library and utilites

  • bowtie, sequence read mapper

  • cufflinks, RNA-Seq differential expression analysis

  • tophat, splice junction mapper

  • bioconductor, meta-package for R bioinformatics

  • BLAST+, sequence alignment tool. (well actually we have older version)

  • GraphViz, graph visiualization toolkit

  • librdf, RDF toolkit

  • UCSC Genome Browser, various utilities and libraries from UCSC

  • eXpress, Streaming quantification for high-throughput sequencing

  • Python packages

WoldlabWiki: Documentation/InstalledSoftware (last edited 2012-09-17 17:49:32 by hamrhein)