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  * [[http://genome.ucsc.edu | UCSC Genome Browser]], various utilities and libraries from UCSC
  		   * [[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
  * [[http://matplotlib.sourceforge.net | matplotlib ]], python plotting library
  * [[http://numpy.scipy.org | NumPy ]], python scientific computing package

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)

  • Network X, python graph library

  • PyGraphViz, python bridge to graphviz

  • GraphViz, graph visiualization toolkit

  • librdf, RDF toolkit

  • UCSC Genome Browser, various utilities and libraries from UCSC

  • eXpress, Streaming quantification for high-throughput sequencing

  • matplotlib, python plotting library

  • NumPy, python scientific computing package

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