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  * [[http://samtools.sourceforge.net/ | samtools ]], SAM/BAM file library and utilites
  * [[http://bowtie-bio.sourceforge.net/index.shtml | bowtie ]], sequence read mapper
  * [[http://cufflinks.cbcb.umd.edu/ | cufflinks ]], RNA-Seq differential expression analysis
  * [[http://tophat.cbcb.umd.edu/ | tophat ]], splice junction mapper
  * [[http://www.bioconductor.org/ | bioconductor ]], meta-package for R bioinformatics		   * [[http://samtools.sourceforge.net/ | samtools ]], (1.18), SAM/BAM file library and utilites
  * [[http://bowtie-bio.sourceforge.net/index.shtml | bowtie ]], (0.9.9.2), sequence read mapper
  * [[http://cufflinks.cbcb.umd.edu/ | cufflinks ]] (1.3.0), RNA-Seq differential expression analysis
  * [[http://tophat.cbcb.umd.edu/ | tophat ]], (1.3.3) splice junction mapper
  * [[http://cran.stat.ucla.edu/banner.shtml | R CRAN home page]], (latest) installable R packages
  * [[http://www.bioconductor.org/ | bioconductor ]], (latest) meta-package for R bioinformatics
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  * [[http://networkx.lanl.gov/ | Network X]] graph library
  * [[http://networkx.lanl.gov/pygraphviz/ | PyGraphViz]] python bridge to graphviz
 * [[http://www.graphviz.org/ | GraphViz ]] graph visiualization toolkit		   * [[http://www.graphviz.org/ | GraphViz ]], graph visiualization toolkit
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  * [[http://genome.ucsc.edu | UCSC Genome Browser ]], various utilities and libraries from UCSC
  * [[http://bio.math.berkeley.edu/eXpress | eXpress ]], Streaming quantification for high-throughput sequencing

  * 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, (1.18), SAM/BAM file library and utilites

  • bowtie, (0.9.9.2), sequence read mapper

  • cufflinks (1.3.0), RNA-Seq differential expression analysis

  • tophat, (1.3.3) splice junction mapper

  • R CRAN home page, (latest) installable R packages

  • bioconductor, (latest) 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)