= Installed Software =

Information about the extra software packages we have installed.

  * [[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
  * [[http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download | BLAST+]], sequence alignment tool. (well actually we have older version)
  * [[http://www.graphviz.org/ | GraphViz ]], (>2.20.2) graph visualization toolkit
  * [[http://librdf.org/ | librdf ]], RDF toolkit
    * 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
    * [[http://code.google.com/p/pysam/ | Pysam ]], (>= 0.6), python interface to sam/bam files