Differences between revisions 1 and 12 (spanning 11 versions)
⇤ ← Revision 1 as of 2012-09-11 18:42:16 →
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Editor: diane
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← Revision 12 as of 2012-09-11 22:53:42 → ⇥
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Editor: hamrhein
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Deletions are marked like this. Additions are marked like this.
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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 ]], (0.1.18), SAM/BAM file library and utilites
  * [[http://bowtie-bio.sourceforge.net/index.shtml | bowtie ]], (0.12.7), sequence read mapper
  * [[http://cufflinks.cbcb.umd.edu/ | cufflinks ]] (1.3.0), RNA-Seq differential expression analysis
  * [[http://tophat.cbcb.umd.edu/ | tophat ]], (1.4.0) 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 ]], (>2.20.2) graph visualization toolkit
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    * redland / librdf (> 1.0.14)
    * redland language binding, python (> 1.0.14)
    * libraptor (> 2.0.6)
    * librasqal (> 0.9.28)
  * [[http://genome.ucsc.edu | UCSC Genome Browser ]], (v272) various utilities and libraries from UCSC
  * [[http://bio.math.berkeley.edu/eXpress | eXpress ]], (1.1.1) Streaming quantification for high-throughput sequencing

  * Python packages
    * [[http://matplotlib.sourceforge.net | matplotlib ]], (> 0.99.1.2) python plotting library
    * [[http://numpy.scipy.org | NumPy ]], (> 1.3.0) python scientific computing package
    * [[http://networkx.lanl.gov/ | Network X]], (> 0.99) python graph library
    * [[http://networkx.lanl.gov/pygraphviz/ | PyGraphViz]], (> 0.99) python bridge to graphviz
    * [[http://ipython.org/ | ipython ]], (> 0.12), enhanced python shell

Installed Software

Information about the extra software packages we have installed.

  • samtools, (0.1.18), SAM/BAM file library and utilites

  • bowtie, (0.12.7), sequence read mapper

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

  • tophat, (1.4.0) 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, (>2.20.2) graph visualization toolkit

  • librdf, RDF toolkit

    • redland / librdf (> 1.0.14)

    • redland language binding, python (> 1.0.14)

    • libraptor (> 2.0.6)

    • librasqal (> 0.9.28)

  • UCSC Genome Browser, (v272) various utilities and libraries from UCSC

  • eXpress, (1.1.1) Streaming quantification for high-throughput sequencing

  • Python packages

    • matplotlib, (> 0.99.1.2) python plotting library

    • NumPy, (> 1.3.0) python scientific computing package

    • Network X, (> 0.99) python graph library

    • PyGraphViz, (> 0.99) python bridge to graphviz

    • ipython, (> 0.12), enhanced python shell

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