Differences between revisions 4 and 5
⇤ ← Revision 4 as of 2012-09-11 19:43:22 →
Size: 1187
Editor: hamrhein
Comment:
← Revision 5 as of 2012-09-11 19:48:33 → ⇥
Size: 1347
Editor: hamrhein
Comment:
Deletions are marked like this. Additions are marked like this.
Line 17: Line 17:
  * [[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)